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

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

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

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 acquisition cost of the vaccine via the NCPDP D.0 claim format. In the Claim Segment field 436-E1 (Product/Service ID Qualifier), a value of "08" (CPT) 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 value of "08" (CPT), 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 (Scheduled 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
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 $172.50
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 $77.00
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 $115.00
91321** Moderna SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 25 mcg/0.25 mL dose, for IM use $128.00
91322** Moderna SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 50 mcg/0.5 mL dose, for IM use $129.50

*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 are available through the VFC program. 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.

Questions and Additional Information