A Pharmacy Automated Accounts Receivable (PAR) System and Methods allows a pharmacy drug store chain to manage, track, and reconcile third party payor receivables associated with prescription transactions. The PAR system obtains and uses data types including, but not limited to, prescription claim data, third party deposit data, third party payor data, and remittance advice data. The data obtained is configured into a PAR database to form PAR data that is used for automatically reconciling third party payor receivables associated with prescription transactions.