New York State Medicaid Coverage Policy and Billing Guidance for Pharmacy Providers for the 2025-2026 COVID-19 Vaccines

  • Guidance is also available in Portable Document Format (PDF)

Effective September 1, 2025, NYRx, the New York State Medicaid pharmacy program is providing coverage for the 2025-2026 formulations of the COVID-19 vaccine.

In accordance with the Executive Order #52 signed by Governor Hochul and the guidance issued by the Commissioner of Health, pharmacists are authorized to order patient-specific orders for COVID-19 vaccination for patients aged 3 and older for off-label use of the COVID-19 vaccine, effective September 5, 2025 , through October 5, 2025, or any subsequent extensions. See Advisory Immunization Notification titled 2025-2026 COVID-19 Guidance for Pharmacists.

Additionally, the Commissioner has available Standing Orders for the COVID-19 vaccines for the Food and Drug Administration (FDA) approved uses, see the details for each found here.

Enrolled pharmacy providers will be reimbursed for vaccine cost and administration when administered to eligible members.

NYRx Vaccine Billing Guidance

This billing guidance may be subject to change. Please continue to monitor New York State Medicaid for both general and COVID-19 vaccine guidance for updates to reimbursement and/or billing instructions. Until further notice, there are two methods of billing vaccines:

  1. National Drug Codes (NDCs) - Preferred method for adult vaccine claims and Vaccines for Children (VFC) enrolled provider claims
    • ⮚ The Medicaid Pharmacy List of Reimbursable Drugs will contain those vaccine NDCs which may be billed to NYRx. The full list can be found by searching at the following website: eMedNY Medicaid Pharmacy List of Reimbursable Drugs.
    • ⮚ NDC billing information can also be found in the following notice
  2. Procedure Codes- Required method for non-VFC enrolled pharmacies submitting COVID-19 claims for persons under 19 years of age

COVID-19 Vaccine Specific

Ordered by a Licensed Pharmacist:

  • ⮚ Pharmacists ordering a vaccine according to the limitations within the Executive order and Commissioner's advisory will submit the claim with the pharmacy National Provider ID number (NPI) in the prescriber ID field.

Ordered by a Patient-Specific or Standing Order:

  • ⮚ Pharmacists will submit the claim pursuant to the standing order or patient-specific order with the prescriber's NPI in the prescriber ID field.
Pharmacies must submit claims for vaccines via the National Council for Prescription Drug Programs (NCPDP) D.0 claim format using the appropriate values. See table below:
NCPDP D.0 Claim Segment Field NDC Billing Value (Preferred Method) Procedure Billing Value
436-E1 (Product/Service ID Qualifier) "03" "09"
407-D7 (Product/Service ID) NDC of vaccine administered* Code of Vaccine or administration
442-E7 (Quantity Dispensed) Numeric Volume "1"
405-D5 (Day Supply) "1" "1"
411-DB (Prescriber ID) Prescriber or Pharmacy NPI** Prescriber or Pharmacy NPI**
444-E9 (Pharmacist ID) Pharmacist NPI Pharmacist NPI

*Vaccine administration fee is included in the reimbursement when billing vaccine as an NDC.
** Dependent on if the vaccine is ordered by a pharmacist or via Patient-Specific/Standing Order

Please see the NYS Medicaid Pharmacy Manual Policy Guidelines document for further guidance on origin code and serial number. Enter a value of "5" in field 419-DJ (Prescription Origin Code) and a value of "99999999" in field 454- EK (Scheduled Prescription ID Number) for Standing Order or Pharmacist ordered COVID-19 vaccines.
NCPDP D.0 Companion Guide can be found here.

Medicaid Managed Care (MMC) Vaccine Billing

NYRx should be billed for any COVID-19 vaccine administered by a pharmacy provider. For non-pharmacy providers, individual MMC plans should be contacted for their specific reimbursement and billing guidance. Plan information can be found by visiting the following website.

Questions and Additional Information:

  • NYS Executive Order regarding vaccine access found here.
  • NYS Vaccine Standing Orders are found here.
  • NYSDOH notifications, including the several recent ones regarding COVID-19 administration at the pharmacy may be found here.
  • Centers for Disease Control and Prevention information on COVID-19 is found here.
  • The Pharmacists as Immunizer Fact Sheet for NY Medicaid's policy and billing for other vaccines is found here.
  • Procedure codes are found starting on page 23 in the Physician Procedure Code Manual found here.
  • NYRx billing and claim questions should be directed to the eMedNY Call Center at (800) 343-9000.
  • NYRx Pharmacy coverage and policy questions should be directed to the Medicaid Pharmacy Policy Unit by telephone at (518) 486-3209 or by email at NYRx@health.ny.gov.