Pharmacies
Contracts with covered entities are the life’s blood of pharmacy 340B programs. Benefit from existing relationships with hundreds of covered entities to hasten the contracting process
From 340B start up clinical operations support to managing relationships with numerous covered entities, Cooper can provide the niche expertise necessary to initiate and operate a successful 340B service line.
Pharmacies are essential to the 340B ecosystem.
The right contract pharmacy services can improve patient access, strengthen adherence, and deliver sustainable revenue for your partner Covered Entities—without adding unnecessary operational burden. Cooper Strategy helps pharmacies understand 340B pharmacy program requirements, implement compliant workflows, and run a high-yield, audit-ready operation from day one.
How Cooper Strategy Supports Pharmacies
- Explain CE oversight expectations so you align early.
- Stand up compliant data, documentation, and audit workflows.
- Launch with measurable KPIs and continuous optimization.
340B Pharmacy Program Requirements (What Pharmacies Need to Know)
Every contract pharmacy must start with foundational compliance. Cooper aligns your team to the core requirements so your Covered Entity (CE) can prove adherence when HRSA reviews the arrangement.
Registration before dispensing
A contract pharmacy must be registered in OPAIS and active before dispensing 340B drugs for a CE. The CE is responsible for ensuring the arrangement complies with all 340B requirements. (HRSA)
Auditable records & oversight
The CE must keep fully auditable records and remains responsible for preventing diversion and duplicate discounts in contract pharmacy arrangements. HRSA recommends quarterly internal audits and annual independent audits of all utilized contract pharmacies. (HRSA)
Duplicate discount prevention (Medicaid)
To avoid manufacturers paying both a 340B discount and a Medicaid rebate on the same claim, CEs use the Medicaid Exclusion File (MEF) to indicate carve-in billing details for fee-for-service Medicaid; this does not apply to Medicaid MCO claims. Coordination with your CE is critical so billing identifiers match MEF entries. (HRSA)
Patient eligibility
Documentation must show the individual is a patient of the CE—dispensing alone is not sufficient. HRSA’s patient-definition resources and the 1996 guidelines remain the audit touchstone. (HRSA)
340B Pharmacy Regulations
In practice, that means: written contracts with clear roles, CE oversight of TPAs, and documentation that links eligible encounters/prescribers to dispensed drugs. (Federal Register)
Key Implications for Pharmacies
Plan your operational guardrails to match CE accountability. Cooper equips your teams with cross-functional playbooks for registration, Medicaid management, and data stewardship so compliance isn’t left to chance.
The CE—not the TPA or pharmacy—bears the compliance risk, but your processes and data must enable the CE to prove compliance on audit. (HRSA)
Registration timing matters
Contract pharmacy enrollment becomes effective on the first day of the next quarter, so plan buildouts accordingly. (340B Registration)
Medicaid mechanics
Fee-for-service Medicaid relies on the MEF; managed care policies vary by state and payer, requiring clear carve-in/out strategies and data flags. (HRSA)
Becoming a 340B Contract Pharmacy: Step‑by‑Step
Follow a launch plan that satisfies the CE’s oversight while equipping your pharmacy team to operate confidently.
Align with a Covered Entity & execute the contract
Define scope (eligible locations, payers, inventory model, shipping/mailing, specialty), data-sharing, reconciliation, fees, audit rights, and termination. The CE will retain ultimate oversight and documentation duties. (HRSA)
Register in OPAIS (by the CE)
The CE’s Authorizing Official/Primary Contact submits your contract pharmacy registration; once approved, enrollment is effective the first day of the next quarter. Ensure contract terms are final before submission. (340B Registration)
Stand up the data & TPA infrastructure
Map identifiers (NCPDP, NPI, prescriber IDs), eligibility rules, virtual inventory/replenishment logic, and accumulator controls. Configure claim flags for Medicaid carve-in/out to align with the CE’s MEF entries (FFS). (HRSA)
Adopt audit-ready SOPs
Build SOPs for patient definition checks, prescriber/site eligibility, diversion prevention, duplicate discount controls, exception handling, and record retention. Follow HRSA’s recommendation for quarterly internal and annual independent audits. (HRSA)
Go-live with continuous monitoring
Track eligible vs. captured scripts, reversal rates, time-to-replenish, and audit findings. Maintain evidence linking encounters to prescriptions per HRSA resources. (HRSA)
Contract Pharmacy Services (What We Do for Pharmacies)
Cooper Strategy pairs regulatory fluency with purpose-built tooling so pharmacies can scale 340B value without compromising compliance.
01Opportunity & Compliance Readiness
We assess script mix, payer distribution, prescriber geography, and CE alignment to size your 340B opportunity—and close compliance gaps before go-live.
02OPAIS Registration & Launch Support
We coordinate with your CE’s AO/PC to ensure accurate, timely contract pharmacy registration and a clean first-quarter start date. (340B Registration)
03TPA & Data Integration
We configure feeds to the CE’s TPA (or your preferred solution), validate mapping, build exception workflows, and institute audit-ready documentation for patient eligibility and prescriber/location checks. (HRSA)
04Medicaid Duplicate Discount Controls
We align identifiers and claim logic to the CE’s MEF records (for FFS Medicaid) and create state-specific playbooks for MCO handling. (HRSA)
05Audit-Ready by Design
Quarterly internal and annual independent contract pharmacy audits (per HRSA recommendations), plus mock audits that mirror HRSA requests. Our tech compiles one-click bundles for auditors, CFOs, or CE compliance teams. (HRSA)
06Performance Optimization
We track KPIs (capture rate, reversal rate, days-to-reconcile, Medicaid exception rate) and run quarterly sprints to lift compliant capture while lowering overhead.
Proof Point
In one engagement, Cooper discovered a CE lacked CVS contracts despite clear patient overlap. We coordinated and registered 18 CVS locations with HRSA. The result: $200,000+ per month paid to the health center by CVS/Wellpartner—enabled by our network development and execution.
The Pharmacy Impact
Cooper’s engagement model keeps teams focused on patients while our platform handles compliance rigor and performance analytics.
- More eligible prescriptions captured with fewer reversals and cleaner reconciliation.
- Better adherence & access through coordinated refills, telehealth-enabled encounters, and compliant mail dispensing where applicable.
- Lower operational drag because our team and tooling streamline exceptions, documentation, and reporting.
What’s Next
Choose the best starting point for your organization. Cooper tailors each engagement to the maturity of your CE partnerships and the sophistication of your dispensing network.
Talk with Cooper StrategyResources
Dive deeper into Cooper Strategy’s 340B expertise with related guides for hospitals, government agencies, and TPAs.
FAQs
Q1: What are the core 340B pharmacy program requirements for a contract pharmacy?
A: Be registered and active in OPAIS before dispensing; support the CE’s duty to prevent diversion and duplicate discounts; maintain auditable records; and participate in regular internal and independent audits. (HRSA)
Q2: How do we avoid duplicate discounts on Medicaid claims?
A: Coordinate with your CE on carve-in/out strategy and ensure your claim identifiers align with the CE’s entries on HRSA’s Medicaid Exclusion File (FFS only); managed care handling varies by state. (HRSA)
Q3: What proves that a person is a 340B-eligible “patient” of the CE?
A: HRSA’s patient-definition resources (including the 1996 guidelines) guide audits. Documentation must show clinical services from or on behalf of the CE—dispensing alone isn’t enough. (HRSA)
Q4: How long does it take to “go live” after registration?
A: Contract pharmacy enrollment begins on the first day of the next quarter, so plan buildouts and testing accordingly. (340B Registration)
Q5: We already use a TPA. Can Cooper still help?
A: Yes. We integrate with common TPAs, harden your SOPs to reflect HRSA-aligned controls, and run audits/optimization sprints to lift performance without increasing risk. (HRSA)