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Pharmacy Billing Services Billing & RCM Services
Each drug you dispense bills to a PBM, a medical plan or a Medicare equipment contractor, and the wrong route loses the margin. Qualigenix routes every claim, reconciles PBM payments, and keeps your 340B claims compliant. Qualigenix provides pharmacy billing services for retail, specialty, compounding and health-system pharmacies: pharmacy and medical-benefit claim submission, specialty drug prior authorization, PBM payment reconciliation, 340B modifier compliance, and rejection follow-up, delivered remotely to pharmacies in 48 states.
What Pharmacy Billing Covers
Pharmacy billing covers three claim types: pharmacy-benefit claims sent to PBMs in the NCPDP format, medical-benefit drug claims sent to health plans with HCPCS codes and NDCs, and Medicare Part B drugs and supplies sent to Medicare's equipment contractors. Each drug has to go to the benefit that covers it, at the quantity and price the payer allows. Qualigenix routes, submits and reconciles all three. Book a free billing audit: 786-259-0231.
01
NCPDP Claim Accuracy
Pharmacy-benefit claims run in real time through the NCPDP standard. A wrong NDC, quantity, days supply or prescriber ID triggers a rejection at the counter or a recoupment in a later audit.
02
Specialty Drug Prior Auth
Specialty drugs, biologics, non-formulary medications and compounds usually need prior authorization or a formulary exception. A prescription filled before approval is often paid by no one.
03
Pharmacy vs Medical Benefit
Some drugs, especially infused and injected specialty drugs, are covered under the medical benefit rather than the pharmacy benefit. Billing them through the PBM, or the reverse, leads to denials and delayed therapy.
04
PBM Underpayments
PBMs pay against contract pricing and maximum allowable cost lists that change often. Payments that come in below contract go unnoticed unless every remittance is matched to the expected rate.
05
Multi-Payer Coverage
Patients may have commercial coverage, Medicare Part B, Part D and Medicaid at once. Billing in the wrong order, or without the primary payer's response, stalls payment.
06
Prescription and Delivery Records
PBM audits and Medicare reviews ask for valid prescriptions, signature logs, proof of delivery and refill records. Missing records turn paid claims into recoupments.
07
Claim Rejections
Common rejections include refill too soon, plan limitations exceeded, NDC not covered and prior authorization required. Many are fixable on the same day if someone works them.
08
340B and PBM Audits
Since January 1, 2025, CMS has required the TB modifier on separately payable Part B drugs acquired through the 340B program. Medicaid duplicate-discount rules and PBM audit terms add their own requirements.
PRECISION: WHAT QUALIGENIX DOES
How Qualigenix Protects Pharmacy Reimbursement
Qualigenix handles routing first, so each claim reaches the benefit that will pay it.
NCPDP and Medical Charge Entry
We submit pharmacy claims in NCPDP format and medical-benefit claims with HCPCS codes, NDCs and units, checking each field before submission.
Specialty PAs and Exceptions
We submit prior authorizations and formulary exceptions with the clinical information payers require and track each approval and renewal date.
Benefit Routing
Each drug is checked against the patient's pharmacy and medical benefits, and medical-benefit drugs are crosswalked from NDC to the right HCPCS code and unit.
PBM Reconciliation
Every PBM remittance is matched to the expected contract price, and underpayments are disputed or flagged for contract review.
Coverage Checks
Coverage and coordination of benefits across commercial, Medicare and Medicaid plans are verified before dispensing.
Proof-of-Delivery Support
Prescription, signature and delivery records are tracked for each claim so they're ready when an audit request arrives.
Rejection Rework
Rejections are worked by reason code, corrected and resubmitted, and denials are appealed where the record supports payment. Qualigenix overturns 79% of the denials it works.
340B and Audit Monitoring
340B claims are checked for the TB modifier and duplicate-discount rules, and audit requests are answered with complete records.
Claims, AR and Margin Reporting
Unpaid claims are worked before they age, and reports show margin by payer, PBM and drug. Find out what your PBM remittances are missing. Qualigenix reviews a sample of your pharmacy claims at no cost. Call 786-259-0231. HIPAA-compliant, with 79% of denials overturned.
CASE STUDY 01
How A Retail and Community Pharmacy Recovered $142K On Benefit-Type Misrouting
THE SITUATION
Provider-administered specialty drugs were billed to the pharmacy (NCPDP) benefit and denied, when they should have been billed to the medical benefit as J-code buy-and-bill, and 340B claims lacked the JG/TB modifier.
WHAT QUALIGENIX DID
We routed provider-administered drugs to the medical benefit with correct J-codes, applied 340B modifiers (JG/TB), and reconciled benefit determination before dispensing.
Key Outcomes & Turnaround
Audited Practice Results
How A Specialty Pharmacy Recovered $127K On Specialty-Claim Backlog
THE SITUATION
Specialty and buy-and-bill drug claims aged after a billing gap, with rebate and reconciliation incomplete and a large balance.
WHAT QUALIGENIX DID
We cleared the backlog, reconciled drug units and rebates, and set a daily claim cadence across benefit types.
Key Outcomes & Turnaround
Audited Practice Results
How A Hospital and Health-System Pharmacy Recovered $119K On High-Cost Drug Authorization
THE SITUATION
How A Hospital and Health-System Pharmacy Recovered $119K On High-Cost Drug Authorization
WHAT QUALIGENIX DID
We added pre-dispense authorization and formulary verification for high-cost drugs and tracked renewals.
Key Outcomes & Turnaround
Audited Practice Results
Pharmacy Billing for Every Service You Provide
Prescription Dispensing (NCPDP)
Retail and mail-order prescriptions billed to PBMs in real time.
COMPLIANCE
How We Keep Pharmacy Billing Compliant
Qualigenix bills pharmacy claims within the rules that govern each one: the TB modifier on 340B-acquired Part B drugs, Medicaid duplicate-discount rules, DMEPOS proof-of-delivery and refill rules, JW and JZ wastage reporting on single-dose containers, and PBM audit requirements. All work is HIPAA-compliant.
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Why Pharmacies Choose Qualigenix
Pharmacies choose Qualigenix because it routes and documents each drug claim correctly, which is where CMS finds most pharmacy payment errors on Medicare equipment-contractor claims.
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Denials overturned on appeal
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QUESTIONS BUYERS ASK
Frequently Asked Questions
Qualigenix prices pharmacy billing after reviewing your claim volume, drug mix and payer mix. A free billing audit gives you a quote and checks your PBM payments for underpayments. Call 786-259-0231 to start.
We submit prior authorizations and formulary exceptions with the clinical information the plan requires, track approvals and renewal dates, and alert your team before an approval lapses.
We apply the TB modifier CMS has required on 340B-acquired Part B drugs since January 1, 2025, and check claims against Medicaid duplicate-discount rules before submission.
Yes. Qualigenix works rejected and unpaid claims by reason code, corrects and resubmits them, and appeals where the record supports payment. Most pharmacies start with a free claims review.
Yes. Qualigenix submits pharmacy-benefit claims to PBMs in NCPDP format and medical-benefit drug claims to health plans with HCPCS codes and NDCs, and routes each drug to the benefit that covers it.
Yes. Every PBM remittance is matched to the expected contract price, and underpayments are disputed with the PBM or flagged for contract review.
Qualigenix works with the pharmacy and EHR systems pharmacies already use and bills from your existing data. We confirm access and workflow during onboarding.
Qualigenix onboards new clients in 6 days on average. Call 786-259-0231 to set a start date.