A computer system and methods manages dispensing and replenishment of medications by a Contract Pharmacy for a Covered Entity. Participating Contract Pharmacies are associated with a Covered Entity, and each medication unit is associated with a code that corresponds to medication units dispersed by the Contract Pharmacies. The amount of medication units corresponding to the code and dispersed by the Contract Pharmacies is tracked. When the amount of medication units dispensed across the Contract Pharmacies to patients of the Covered Entity reaches a replenishment threshold, replacement medication units are ordered to replace inventory loaned by the Contract Pharmacies to the Covered Entity at the Covered Entity's available drug discount purchase price.