A system and method for optimized management of pharmacy workflow, specifically, workflow associated with fulfillment of prescription orders for medications and health-related products in a pharmacy environment. A computer-controlled system coordinates and controls pharmacy workflow to sequence prescriptions for fulfillment in a most efficient path thereby minimizing a cost function associated with fulfillment of the prescription order. The system coordinates and controls prescription order fulfillment from automated and non-automated storage locations and can be easily adapted to the specific layout and level of automation desired by the operator.