UPDATE: Medicaid Coverage for the 2023-2024 COVID-19 Vaccines for Pharmacy Providers Not Enrolled in the Vaccines for Children (VFC) Program

See important update regarding the 2024-2025 vaccine season.
  • Guidance is also available in Portable Document Format (PDF)

Effective 11/14/2023, in an effort to enhance access to COVID-19 vaccines for children and adolescents, New York State Medicaid will nowreimburse qualified pharmacy providers that are not enrolled in the VFC program for the actual acquisition cost of the COVID-19 vaccine and its administration when administered to members younger than 19 years of age during the 2023-2024 vaccine season.

Billing Instructions for Providers Enrolled in the VFC Program

VFC-enrolled providers should continue to bill NYRx for VFC-provided vaccines by submitting the procedure code “90460” for administration and the appropriate COVID-19 vaccine procedure code from the table below. Reminder: VFC-enrolled providers are responsible for ordering and utilizing VFC stock and should not bill a cost for VFC-obtained vaccine to the Medicaid program.

Billing Instructions for Providers Not Enrolled in the VFC Program

Providers that do not participate in the VFC program will submit the procedure code “90460” for the administration of a VFC-eligible vaccine and the appropriate COVID-19 vaccine procedure code from the table below, with the actual acquisition cost of the vaccine. NYS Medicaid will reimburse $25.10 for the administration of VFC-eligible vaccines to Medicaid members under 19 years of age. Pharmacy providers enrolled in NYS Medicaid are responsible for ensuring appropriate billing for members younger than 19 years of age. Claims submitted with incorrect data for vaccine cost and/or administration of the COVID-19 vaccine are subject to audit and recovery.

In addition to the procedure code for administration, providers will submit the procedure code for the COVID-19 vaccine from the table below, with acquisition cost as appropriate.

Table 1

Procedure Code Manufacturer & COVID-19 Vaccine Procedure Code Descriptions
91304 SARS-COV-2 (COVID-19) vaccine, subunit, recombinant spike protein- nanoparticle+Matrix-M1 Adjuvant, preservative-free, five mcg/0.5 mL dose
91318 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative- free, tris-sucrose, three mcg/0.3 mL dose
91319 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative- free, tris-sucrose, ten mcg/0.3 mL dose
91320 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative- free, tris-sucrose, 30 mcg/0.3 mL dose
91321 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative- free, 25 mcg/0.25 mL dose
91322 SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative- free, 50 mcg/0.5 mL dose

NYRx Billing Instructions for Pharmacies Not Enrolled in the VFC Program

The pharmacy must submit the claim for the vaccine and administration via the NCPDP D.0 claim format. In the Claim Segment field 436-E1 (Product/Service ID Qualifier), the applicable value for vaccine or administration will qualify the code submitted in field 407-D7 (Product/Service ID) as a procedure code. The applicable procedure code for administration or the vaccine will be submitted in field 407-D7 (Product/Service ID). Pharmacies will bill with a quantity of "1" and a day supply of "1" for each dose, regardless of volume.

Table 2

NCPDP D.0 Claim Segment Field Value
436-E1 (Product/Service ID Qualifier) Enter the applicable value, which qualifies the code submitted in field 407-D7 (Product/Service ID) as a procedure code.
407-D7 (Product/Service ID) Enter the administration code and/or applicable vaccine procedure code listed in Table 1 above.
442-E7 (Quantity Dispensed) Enter the value of "1"
405-D5 (Day Supply) Enter the value of "1"
444-E9 (Pharmacist ID) Enter the pharmacist's NPI number
411-DB (Prescriber ID) Enter the dispensing pharmacy's NPI number*

*If the vaccine is ordered by a prescriber and not the pharmacist, please enter the prescriber's NPI number.

Please see the NYS Medicaid Pharmacy Manual Policy Guidelines for further guidance on origin code and serial number values that must be submitted on the claim for "pharmacy dispensing" when applicable for non-patient-specific orders. 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). NCPDP D.0 Companion Guide can be found here.

Additional Guidance for Providers Not Enrolled in the VFC Program

Please be advised that reimbursement for the cost of COVID-19 vaccines for Medicaid members younger than 19 years of age is subject to change. The Department is encouraging Medicaid providers to enroll in the VFC program for continued provision of VFC-eligible vaccines to members younger than 19 years of age. Additional information for enrollment, based on location, can be found at the following links:

Medicaid Managed Care (MMC) COVID-19 Vaccine Billing

NYRx should be billed for any COVID-19 vaccine administered by a pharmacy provider. For non- pharmacy providers, MMC reimbursement, billing, and/or documentation requirement questions should be directed to the specific MMC Plan of the enrollee. MMC Plan information can be found by visiting the following website.

Additional Information