Typically a patient will receive his/her co-pay card from their physician along with a prescription for the medicine. The patient takes the card and prescription to a pharmacy where the pharmacist enters processing information into his/her pharmacy management system to submit a claim.

If a patient has insurance, the pharmacist will key in the patient's insurance number in the primary field and an identifier from the co-pay card into the secondary insurer field. Instantaneously the pharmacy benefit manager provides coverage data, relaying the patient's out of pocket, or co-pay to the secondary insurer's benefit manager, who then provides a discount accordingly.^{[citation needed]}

An example: A brand offers a co-pay card giving patients the opportunity to save up to $20 off each prescription fill. A patient receives the co-pay card and visits their pharmacy. The patient provides his insurance card and co-pay card to the pharmacist. The pharmacist enters information into his pharmacy management system from both cards. The insurance benefit manager recognizes the drug as a TIER 3 brand for the patient and relays the patient co-pay to be $30.00. The co-pay card benefit manager recognizes the $30.00 and covers the $20.00 of co-pay, leaving $10 for the patient to pay out of pocket. Another patient without prescription insurance coverage follows the same process. The co-pay card takes the primary insurer position where it recognizes the claim as that of a cash-paying patient and applies $20.00 discount to the patient's out-of-pocket costs.^{[citation needed]}

In most cases the service provider of the co-pay card program holds a reimbursement account for the pharmaceutical marketing client, which is used to remit to pharmacies the cost reductions through co-pay card programs. The co-pay service provider remits to pharmacies every 14 to 28 days and deducts these remittances via this account.

Some providers have attempted a variation on the original co-pay card by going to a magnetic strip swipe process, by which the card runs through both the pharmacy software and financial software (e.g. Visa/MasterCard and Debit networks).

Debit cards are another reimbursement method for co-pay in pharmacies because they offer real-time reimbursement of co-pay claims. However, with new prompt-pay regulations for adjudicators, required for Medicare Part D and implemented by most PBMs, few pharmacies wait more than one week for reimbursement. Pharmacies used to prefer real-time Debit payments because they didn't require the pharmacies to carry the "float" of the 14 to 28 days payment cycles. This is no longer true.