New York State Medicaid Coverage Policy and Billing Guidance for the 2023-2024 COVID-19 Vaccines

Guidance updated and replaced, see NYRx, the New York State Medicaid Pharmacy Program Pharmacists as Immunizers Fact Sheet
  • Guidance is also available in Portable Document Format (PDF)

Effective September 11, 2023, NYRx, the New York State Medicaid Fee-for-Service pharmacy program, reimburses enrolled and qualified pharmacy providers for COVID-19 vaccines and their administration as approved by the FDA or authorized for emergency use, and recommended by the Advisory Committee on Immunization Practices (ACIP) of the Centers for Disease Control (CDC).

This billing guidance may be subject to change. Please continue to monitor New York State Medicaid COVID-19 vaccine guidance for updates to reimbursement and/or billing instructions.

NYRx Billing Instructions for Qualified Pharmacies:

Pharmacies will submit the administration fee and, when applicable, the actual acquisition cost of the vaccine via the NCPDP D.0 claim format. In the Claim Segment field 436-E1 (Product/Service ID Qualifier), the applicable value 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 1
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 2 below
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 being ordered by a prescriber and not the pharmacist, please enter the prescriber's NPI number.

Please see the NYS Medicaid Pharmacy Manual Policy Guidelines document 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 (Sched uled Prescription ID Number).
NCPDP D.0 Companion Guide can be found here.

Pharmacies will submit the administration and corresponding vaccine codes from Table 2 below in field 407-D7 (Product/Service ID) as noted in Table 1.

Table 2
CPT Code Manufacturer & COVID-19 Vaccine CPT Code Descriptions Fee per Dose
90480* Immunization administration by intramuscular (IM) injection of SARS-CoV-2 (COVID-19) vaccine, single dose $40.00
91304** Novavax SARS-COV-2 (COVID-19) vaccine, subunit, recombinant spike protein-nanoparticle+Matrix-M1 Adjuvant, preservative free, 5 mcg/0.5 mL dose, for IM use Cost
91318** Pfizer-BioNTech SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 3 mcg/0.3 mL dose, for IM use Cost
91319** Pfizer-BioNTech SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 10 mcg/0.3 mL dose, for IM use Cost
91320** Pfizer-BioNTech SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, tris-sucrose, 30 mcg/0.3 mL dose, for IM use Cost
91321** Moderna SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 25 mcg/0.25 mL dose, for IM use Cost
91322** Moderna SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 50 mcg/0.5 mL dose, for IM use Cost

*CPT code 90480 is submitted for administration of any COVID-19 vaccine in the table above for individuals 19 years of age and older.

**Note: COVID-19 vaccines are available to members younger than 19 years of age through the Vaccines for Children (VFC) program. Pharmacies may not bill Medicaid for the cost of vaccines that have been obtained via the VFC program. Limited to the 2023-2024 vaccine season, non-VFC enrolled pharmacies, may bill the COVID-19 vaccine per the guidance posted here. Pharmacy providers, whether enrolled in the VFC program or not, must submit the administration code "90460" for administration of a VFC-eligible vaccine and the applicable vaccine code from Table 2 with an ingredient cost of $0.00. Procedure code "90460" has a fee of $25.10.

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.

COVID-19 Vaccine Counseling:

Pharmacists offering COVID-19 vaccine counseling services to members under 21 years of age can reference the coverage and reimbursement policy outlined in the Updated COVID-19 Vaccine Counseling Coverage found here.

Questions and Additional Information: