A system and method are provided for processing flexible spending account transactions involving a plurality of pharmacies, a service provider, one or more pharmacy benefits managers ("PBMs"), and individuals having flexible spending accounts ("FSAs") and stored value cards for debiting their FSAs. The service provider maintains a PBM transaction database; receives from a pharmacy an authorization request at the time of purchase; queries the PBM transaction database for a matching transaction in response to the authorization request; and authorizes payment of the patient responsible balance to be automatically debited against the respective FSA at the time of purchase.