Specialty Pharmacy Management Software: Oncology, HIV, and High-Cost Medications 2026

Specialty pharmaceuticals represent over 50% of total drug spending in 2026 despite comprising less than 2% of prescriptions, with oncology, biologics, and gene therapies commanding prices of $50,000-$500,000+ per patient annually. Specialty pharmacy management software has evolved into sophisticated platforms managing the entire patient journey—from prior authorization and financial assistance to adherence monitoring and outcomes tracking. This comprehensive guide covers specialty pharmacy software, disease-specific workflows, payer navigation, and building profitable specialty services.

The Specialty Pharmacy Market 2026

Market Size and Growth

Explosive Growth:

• Global Specialty Drug Market: $530 billion in 2026, growing at 10-12% CAGR
• U.S. Specialty Pharmacy Market: $300+ billion, 55% of total drug spend
• Emerging Markets: Fastest growth in Africa, Latin America, Asia-Pacific as access improves

Therapeutic Categories:

• Oncology: $210 billion (40% of specialty spend) - immunotherapies, targeted agents, CAR-T
• Immunology: $110 billion - rheumatoid arthritis, psoriasis, IBD biologics
• HIV/AIDS: $35 billion - antiretroviral therapy combinations
• Hepatitis C: $15 billion - direct-acting antivirals (DAAs)
• Multiple Sclerosis: $25 billion - disease-modifying therapies
• Gene Therapies: $5 billion and growing rapidly (Zolgensma $2.1M, Hemgenix $3.5M)

Specialty Drug Characteristics

Defining Features:

• High Cost: Average annual cost $80,000-$100,000+ per patient
• Complex Administration: Injectable, infused, or requiring special handling
• Limited Distribution: Restricted to specialty pharmacies
• Intensive Services: Patient education, adherence support, side effect management
• REMS Requirements: Risk Evaluation and Mitigation Strategies for certain drugs
• Prior Authorization: Nearly universal payer requirement
• Patient Assistance: Financial support programs from manufacturers essential

Leading Specialty Pharmacy Software Platforms 2026

1. AllianceRx Walgreens Prime (Platform)

Overview: Integrated specialty pharmacy platform from major PBM/specialty pharmacy.

Key Features:

• Comprehensive specialty pharmacy management
• Prior authorization automation
• Patient assistance program integration
• Adherence monitoring and interventions
• Clinical programs by disease state
• Manufacturer hub services
• Data analytics and reporting

Ideal For: Large specialty pharmacy operations or outsourcing to AllianceRx

2. Accredo Specialty Pharmacy (Evernorth/Cigna)

Overview: Leading specialty pharmacy with proprietary technology platform.

Key Features:

• Disease-specific clinical programs (oncology, MS, rheum, etc.)
• Dedicated care teams (pharmacists, nurses, social workers)
• Prior authorization management
• Financial assistance coordination
• Patient education and training (self-injection, infusion)
• Outcomes tracking and reporting

Ideal For: Health plans and providers partnering with Accredo for specialty services

3. BioPlus Specialty Pharmacy

Overview: Independent specialty pharmacy network with technology platform.

Key Features:

• Network of 3,000+ independent pharmacies offering specialty services
• Central patient intake and coordination
• Prior authorization support
• Buy-and-bill pharmacy services for physician offices
• Clinical management programs
• Technology platform for member pharmacies

Ideal For: Independent pharmacies joining specialty pharmacy network

4. Omnicare Specialty Care (CVS Health)

Overview: Specialty pharmacy for complex conditions within CVS Health ecosystem.

Key Features:

• Oncology, transplant, infectious disease focus
• 24/7 pharmacist support
• Home delivery
• Hub services for patient start forms
• Clinical and reimbursement services
• Integration with CVS retail and mail order

Ideal For: Integration with CVS/Caremark PBM clients

5. PioneerRx Specialty Module

Overview: Specialty pharmacy functionality within community pharmacy management system.

Key Features:

• Specialty drug inventory management
• Prior authorization tracking
• Patient assistance program management
• Copay accumulator tracking
• Clinical documentation for specialty services
• Financial tracking and profitability analysis

Ideal For: Independent community pharmacies adding specialty services

6. PharmaPOS Specialty Pharmacy Module

Overview: Specialty pharmacy management within comprehensive pharmacy platform for global markets.

Key Features:

• High-cost medication inventory tracking
• Prior authorization workflow management
• Patient assistance program coordination
• Adherence monitoring and interventions
• Payer-specific formulary management
• Clinical intervention documentation
• Financial analysis per specialty patient
• One-time licensing: ₦450,000 - ₦1,350,000 (no monthly fees)
• Offline capability: Continued operation during internet outages
• Emerging markets focus: Designed for Africa, Latin America, Asia-Pacific

Ideal For: Pharmacies in developing markets offering specialty services

Essential Specialty Pharmacy Software Features

1. Patient Intake and Enrollment

Referral Management:

• Electronic referrals from prescribers
• Fax/phone intake processes
• Patient demographic collection
• Insurance verification
• Medical history and comorbidities
• Allergy documentation
• Consent and privacy agreements (HIPAA)

Prescription Capture:

• E-prescribing integration
• Prior authorization prescription requirements
• Diagnosis code documentation (ICD-10)
• Clinical justification for therapy

Insurance Verification:

• Real-time eligibility checking
• Medical vs. pharmacy benefit determination (buy-and-bill vs. traditional fill)
• Specialty tier identification
• Deductible and out-of-pocket maximums
• Prior authorization requirements by payer

2. Prior Authorization Management

PA Workflow:

• Automated PA requirement identification
• Electronic PA submission (CoverMyMeds, Surescripts)
• Clinical documentation compilation
• Peer-to-peer scheduling for denials
• Appeal management
• PA status tracking
• Approval/denial notifications

Clinical Documentation:

• Diagnosis codes and disease severity
• Previous therapy trials and failures (step therapy documentation)
• Lab values and diagnostic test results
• Clinical notes from prescriber
• Evidence-based guideline citations

Turnaround Time Tracking:

• Time from prescription to PA submission
• Time from PA submission to decision
• Bottleneck identification
• Payer performance tracking

3. Patient Assistance and Financial Programs

Manufacturer Copay Cards:

• Copay card enrollment and application
• Real-time adjudication at point of sale
• Secondary billing to manufacturer program
• Accumulator bypass tracking
• Maximum benefit tracking

Patient Assistance Programs (PAPs):

• Free drug programs for uninsured/underinsured
• Application submission and status tracking
• Eligibility verification (income, insurance)
• Medication dispensing from PAP inventory
• Re-enrollment management (annual recertification)

Foundation Grants:

• Independent charitable foundations (e.g., HealthWell, PAN)
• Disease-specific funds
• Application submission
• Grant approval tracking
• Fund depletion monitoring

Specialty Pharmacy Discount Programs:

• Manufacturer bridge programs (30-60 days while PA processed)
• Pharmacy-sponsored discount programs
• Cash pricing alternatives

4. Specialty Drug Inventory Management

High-Value Inventory:

• Lot-specific tracking for specialty medications
• Refrigerated storage monitoring (2-8°C temperature logs)
• Expiration date management (short-dated specialty drugs)
• Controlled distribution tracking
• Serialization and pedigree (drug supply chain security)

Wholesaler Coordination:

• Limited distribution specialty drug ordering
• Direct-from-manufacturer procurement
• Drop shipment coordination
• Inventory optimization (minimize waste of expensive products)

Cost Accounting:

• Acquisition cost tracking (WAC, AWP, actual purchase price)
• Reimbursement tracking (payer-specific)
• Gross-to-net revenue analysis
• Profitability per specialty patient

5. Clinical Program Management

Disease-Specific Protocols:

• Oncology: Chemotherapy regimen verification, oral chemotherapy adherence, side effect management
• HIV/AIDS: Antiretroviral adherence, resistance testing tracking, CD4/viral load monitoring
• Hepatitis C: Direct-acting antiviral (DAA) adherence, cure rate tracking (SVR12)
• Rheumatology: Biologic DMARD management, infusion scheduling, TB screening tracking
• Multiple Sclerosis: Disease-modifying therapy adherence, relapse tracking, MRI coordination

Patient Education:

• Drug-specific education materials
• Administration technique training (self-injection, infusion)
• Side effect recognition and management
• Drug-drug and drug-food interaction counseling
• Multi-language support

Adherence Monitoring:

• Refill compliance tracking (PDC - Proportion of Days Covered)
• Missed dose identification
• Intervention workflows for non-adherence
• Patient contact (phone, SMS, app) for reminders
• Barriers to adherence assessment (side effects, cost, complexity)

6. Medication Administration and Scheduling

Infusion Coordination:

• Infusion center scheduling
• Home infusion coordination
• Infusion supplies coordination (pumps, tubing, ancillaries)
• Nursing visit scheduling
• Pre-medication protocols

Injection Training:

• Self-injection education (videos, live demonstration)
• Return demonstration verification
• Sharps disposal coordination
• Injection site rotation tracking

Refill Synchronization:

• Automatic refill calculation based on days supply
• Multi-drug regimen coordination (e.g., HIV 3-drug combos)
• Proactive refill outreach
• Delivery scheduling

7. Buy-and-Bill Management

Physician Office Support:

• Medication procurement and delivery to physician office
• Medical benefit billing support (J-codes)
• Reimbursement tracking
• Accounts receivable management
• Prior authorization for medical benefit

Office Inventory Management:

• Consignment inventory tracking at physician practices
• Usage reporting
• Replenishment ordering
• Waste documentation (unused vials)

Revenue Cycle Management:

• Medical claim submission (physician on behalf of patient)
• Payment posting
• Denial management and appeals
• Patient billing for coinsurance/deductibles

8. REMS Program Compliance

Risk Evaluation and Mitigation Strategy (REMS) Tracking:

• REMS-required medications identification (isotretinoin/iPLEDGE, thalidomide/THALOMID REMS, clozapine/Clozapine REMS)
• Patient enrollment in REMS programs
• Prescriber and pharmacy certification
• Required testing and counseling documentation
• Dispensing authorization verification
• Periodic patient surveys and monitoring

Examples:

• iPLEDGE (isotretinoin): Pregnancy testing, two forms of contraception, patient/prescriber/pharmacy registration
• THALOMID REMS (thalidomide, lenalidomide, pomalidomide): Pregnancy prevention, patient surveys
• Clozapine REMS: ANC monitoring for agranulocytosis risk

9. Outcomes Tracking and Reporting

Clinical Outcomes:

• Disease-specific metrics (viral suppression for HIV, SVR12 for HCV, PASI score for psoriasis)
• Medication adherence rates (PDC, MPR)
• Hospitalization and ER visit rates
• Quality of life assessments
• Patient-reported outcomes (PROs)

Financial Outcomes:

• Total cost of care
• Medical cost offsets (reduced hospitalizations)
• Medication costs
• Return on investment for payers and providers

Regulatory Reporting:

• CMS Star Ratings metrics (adherence for diabetes, hypertension, cholesterol meds)
• HEDIS measures
• Accreditation reporting (URAC, ACHC)

Building a Specialty Pharmacy Program

Phase 1: Strategic Planning (Months 1-3)

Market Assessment:

• Patient population analysis (disease prevalence, specialty drug usage)
• Competitor analysis (existing specialty pharmacies in market)
• Payer landscape (insurance coverage, prior authorization requirements)
• Referral source identification (specialty physicians, hospitals)

Service Line Selection:

• Focus areas based on patient need and expertise (oncology, rheumatology, HIV, etc.)
• Resource requirements for each service line
• Profitability analysis per service line

Business Model:

• Retail specialty pharmacy (patient self-administration)
• Infusion center pharmacy
• Buy-and-bill for physician offices
• Home infusion pharmacy
• Hybrid model

Phase 2: Regulatory and Accreditation (Months 3-6)

Licensing:

• State pharmacy license with specialty pharmacy designation (if required)
• Controlled substance registration (DEA)
• Specialty drug distributor agreements (limited distribution drugs)

Accreditation:

• URAC Specialty Pharmacy accreditation
• ACHC (Accreditation Commission for Health Care) specialty pharmacy
• Specialty Pharmacy Accreditation (required by many payers for network participation)

Payer Credentialing:

• Specialty pharmacy network applications
• Medicare Part D specialty pharmacy status
• Commercial payer specialty pharmacy agreements

Phase 3: Infrastructure and Technology (Months 4-7)

Facility:

• Separate specialty pharmacy area (HIPAA privacy for patient consultations)
• Refrigerated storage (2-8°C) with temperature monitoring
• Controlled substance vault (many specialty drugs are Schedule II-V)
• Patient consultation rooms

Technology:

• Specialty pharmacy management software
• Prior authorization automation platform
• Patient assistance program integration
• Clinical documentation system
• Inventory management for high-cost drugs

Staffing:

• Specialty pharmacists with disease-specific training
• Pharmacy technicians (specialty-trained)
• Patient care coordinators
• Prior authorization specialists
• Reimbursement specialists

Phase 4: Clinical Program Development (Months 6-9)

Protocols:

• Disease-specific clinical protocols
• Patient education curricula
• Adherence intervention workflows
• Side effect management algorithms
• Outcomes tracking metrics

Training:

• Pharmacist disease state certification (oncology, HIV, transplant, etc.)
• Patient counseling techniques (motivational interviewing)
• Prior authorization expertise
• Financial assistance navigation
• Infusion training (for infusion specialty pharmacies)

Phase 5: Launch and Growth (Months 9-12+)

Physician Outreach:

• Specialty physician office visits (oncologists, rheumatologists, infectious disease)
• Hospital discharge planners
• Service offerings presentation
• Collaborative agreements

Patient Enrollment:

• Referral intake workflows
• Quick turnaround time (24-48 hours prescription to first fill)
• White-glove patient experience
• 24/7 pharmacist availability

Payer Relationships:

• Specialty pharmacy network participation
• Outcomes data sharing
• Collaborative care programs
• Value-based contracting

Specialty Pharmacy Disease-Specific Workflows

Oncology Specialty Pharmacy

Oral Chemotherapy Management:

• Chemotherapy regimen verification against NCCN guidelines
• Drug-drug interaction screening (chemotherapy + supportive care meds)
• Toxicity monitoring (patient-reported)
• Adherence monitoring (missed doses can reduce efficacy)
• Side effect management (nausea, diarrhea, neuropathy, hand-foot syndrome)

Supportive Care Coordination:

• Anti-emetics for chemotherapy-induced nausea/vomiting
• Growth factors (filgrastim, pegfilgrastim) for neutropenia
• Pain management
• Antidiarrheals and constipation management

Biosimilar Management:

• Substitution of biosimilars for originator biologics (e.g., bevacizumab biosimilars for Avastin)
• Payer formulary requirements
• Patient and prescriber education on biosimilars

HIV/AIDS Specialty Pharmacy

Antiretroviral Therapy (ART) Management:

• Single-tablet regimens (STRs) for adherence optimization
• Resistance testing review before therapy initiation
• CD4 count and viral load monitoring schedules
• Adherence counseling (>95% adherence needed for viral suppression)

Opportunistic Infection Prophylaxis:

• PCP prophylaxis (trimethoprim-sulfamethoxazole, dapsone, atovaquone)
• MAC prophylaxis (azithromycin)
• TB screening and treatment

PrEP (Pre-Exposure Prophylaxis) Services:

• HIV prevention for high-risk individuals (Truvada, Descovy)
• Quarterly HIV testing and STI screening coordination
• Adherence support
• Risk reduction counseling

Hepatitis C Specialty Pharmacy

Direct-Acting Antiviral (DAA) Therapy:

• Genotype-specific regimen selection
• Prior authorization for expensive DAAs ($25,000-$90,000 per course)
• Adherence support (8-12 week regimens, 95%+ adherence needed)
• Drug-drug interaction management (especially with HIV meds)

Cure Monitoring:

• Sustained virologic response (SVR12) tracking (undetectable HCV RNA 12 weeks post-treatment = cure)
• Treatment failure management and retreatment

Rheumatology (Biologics for RA, PsA, AS)

Biologic DMARD Management:

• TNF inhibitors (adalimumab, etanercept, infliximab, golimumab, certolizumab)
• IL-6 inhibitors (tocilizumab, sarilumab)
• IL-17 inhibitors (secukinumab, ixekizumab)
• JAK inhibitors (tofacitinib, upadacitinib, baricitinib)

Safety Monitoring:

• TB screening before biologic initiation (QuantiFERON, PPD)
• Hepatitis B screening
• Infection risk counseling
• Live vaccine avoidance

Self-Injection Training:

• Injection technique education (subcutaneous)
• Injection site rotation
• Sharps disposal
• Refrigerated storage education

Multiple Sclerosis (MS)

Disease-Modifying Therapy (DMT) Management:

• Injectables (interferons, glatiramer acetate)
• Oral therapies (fingolimod, dimethyl fumarate, teriflunomide, siponimod, etc.)
• Infusions (natalizumab, ocrelizumab, alemtuzumab)

Monitoring:

• Relapse tracking
• MRI surveillance coordination
• JC virus testing for natalizumab PML risk
• Lymphocyte count monitoring for fingolimod, alemtuzumab

Adherence:

• Common non-adherence due to injection fatigue or side effects
• Adherence interventions and support
• Switch to alternate DMT if non-adherence persists

Financial Sustainability of Specialty Pharmacy

Revenue Streams

Prescription Dispensing Revenue:

• Pharmacy benefit reimbursement (ingredient cost + dispensing fee)
• Spread between acquisition cost and reimbursement
• High-cost drugs with modest spreads can still be profitable

Medical Benefit (Buy-and-Bill) Revenue:

• Physician practice purchases drug, administers, bills medical insurance
• Specialty pharmacy sources drug, delivers to practice, manages reimbursement
• Revenue share or fee-for-service arrangement

Clinical Service Fees:

• Medication therapy management (MTM) payments
• Comprehensive medication reviews
• Disease management programs (payer-contracted)
• Patient education and training fees

Manufacturer Revenue:

• Hub services fees from manufacturers
• Patient assistance program administration
• Data and outcomes reporting fees
• Adherence program support

Cost Management

Drug Acquisition Optimization:

• Negotiate best pricing with limited distribution wholesalers
• Direct-from-manufacturer purchasing for better pricing
• 340B pricing for eligible covered entities
• Group purchasing organization (GPO) contracts

Inventory Management:

• Just-in-time inventory for expensive specialty drugs
• Patient-specific procurement (order drug after prescription received)
• Minimize waste (short-dated, unused inventory)

Prior Authorization Efficiency:

• Electronic PA automation reducing labor costs
• High first-pass approval rates through clinical expertise
• Reduce delays and lost prescriptions

Staffing Optimization:

• Pharmacist productivity (patients managed per FTE)
• Technician utilization for non-clinical tasks
• Patient care coordinator efficiency

Profitability Analysis

Typical Specialty Pharmacy Metrics:

• Gross Margin: 5-15% (lower than traditional retail 20-25%)
• Revenue per Patient per Year: $80,000-$120,000 average
• Patients per Pharmacist FTE: 150-250 depending on disease complexity
• Operating Margin: 2-8% (labor-intensive services)

Profitability Example (Small Specialty Pharmacy):

• Active Patients: 200
• Average Revenue per Patient: $100,000
• Total Revenue: $20 million
• Gross Margin: 10% = $2 million gross profit
• Operating Expenses: Salaries ($800K), rent/utilities ($100K), technology ($150K), other ($250K) = $1.3M
• Net Operating Income: $700,000
• Operating Margin: 3.5%

Advanced Specialty Pharmacy Technologies 2026

AI-Powered Adherence Prediction

Machine Learning Models:

• Patient risk stratification for non-adherence
• Predictive interventions before adherence lapses
• Personalized outreach strategies
• Optimal contact timing and channel

Remote Patient Monitoring

Connected Devices:

• Smart pill bottles tracking bottle opening
• Injection pens with Bluetooth tracking (doses administered)
• Wearables for symptom tracking (e.g., tremor for Parkinson's)
• Integration with specialty pharmacy platform

Real-Time Alerts:

• Missed dose alerts to pharmacist
• Proactive outreach to patient
• Medication adjustment recommendations

Telepharmacy for Specialty Care

Virtual Consultations:

• Video visits with specialty pharmacists
• Remote patient education and training
• Medication reviews via telehealth
• Expanded access for rural patients

Blockchain for Specialty Drug Supply Chain

Drug Pedigree and Authentication:

• Blockchain-based tracking from manufacturer to patient
• Counterfeit drug prevention
• Serialization and verification
• Temperature excursion tracking

Regulatory Compliance for Specialty Pharmacy

HIPAA Compliance

Privacy Requirements:

• Patient health information protection
• Secure messaging and communication
• Access controls and audit logs
• Business associate agreements with technology vendors

URAC Specialty Pharmacy Accreditation

Requirements:

• Comprehensive clinical programs
• Quality management system
• Patient safety protocols
• Outcomes measurement
• Staff qualifications and training

State Board of Pharmacy Regulations

Compliance:

• Specialty pharmacy license (in states requiring)
• Patient counseling requirements
• Recordkeeping and documentation
• Controlled substance inventory and security
• Temperature monitoring and storage

Medicare Part D Requirements

Compliance:

• MTM program participation
• Star Ratings metrics (adherence measures)
• Coverage determination and appeals processes
• Fraud, waste, and abuse prevention

Getting Started with Specialty Pharmacy Software

Step 1: Define Your Specialty Focus

Assess:

• Patient population needs and disease prevalence
• Physician referral sources and relationships
• Payer landscape and network opportunities
• Competitive landscape

Select Initial Service Lines:

• Start with 1-2 disease states for focused expertise
• Oncology, HIV, rheumatology, MS most common starting points
• Expand over time as programs mature

Step 2: Choose Software Platform

Evaluate:

• Specialty pharmacy-specific features vs. modules on general pharmacy software
• Integration with your existing pharmacy system
• Prior authorization automation capabilities
• Patient assistance program integration
• Clinical documentation and outcomes tracking
• Total cost of ownership

Vendors to Consider:

• Specialty-focused: AllianceRx, Accredo (if partnering)
• Pharmacy system specialty modules: PioneerRx, PharmaPOS
• Standalone specialty platforms

Step 3: Implement and Launch

Build Infrastructure:

• Obtain specialty pharmacy accreditation (URAC)
• Credential with specialty pharmacy networks
• Train staff on disease states and workflows
• Develop clinical protocols

Pilot Launch:

• Start with manageable patient volume
• Refine workflows based on real-world experience
• Gather patient and prescriber feedback
• Measure outcomes and improve

Step 4: Grow and Scale

Marketing:

• Physician outreach and education
• Patient referral sources
• Payer partnerships
• Community awareness

Expand Services:

• Add additional disease states
• Enhance clinical programs
• Develop value-based contracts with payers
• Offer home delivery and infusion services

Conclusion: Specialty Pharmacy as High-Value Service

Specialty pharmacy represents the fastest-growing, highest-value segment of pharmaceutical care in 2026. While complex and resource-intensive, well-executed specialty pharmacy programs generate substantial revenue, improve patient outcomes, and differentiate pharmacies in competitive markets.

Leading specialty pharmacies using advanced software platforms achieve:

• >90% Prior Authorization Approval Rates: Clinical expertise and automation driving approvals
• >85% Medication Adherence: Intensive support improving outcomes
• $100,000+ Revenue per Patient Annually: High-value medication management
• Strong Payer Partnerships: Outcomes data demonstrating value
• Patient Satisfaction: White-glove service experience

Whether you're an independent pharmacy adding specialty services, a health system building in-house specialty pharmacy, or a community pharmacy joining a specialty network, investing in purpose-built specialty pharmacy software enables efficient operations, clinical excellence, and financial sustainability.

Contact MedSoftwares to learn how PharmaPOS Specialty Pharmacy Module can support your specialty pharmacy services with comprehensive patient management, prior authorization workflows, and financial tracking designed for global markets.

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