This paper proposes a novel mathematical model and scheduling system for real pharmaceutical industries (PI). To consider general characteristics of the PI, the proposed model employed a strategy to address a mixed integer linear programming (MILP) formulation. Heuristic techniques were then developed to solve complex scheduling problems for PI such as critical and bottleneck operations. These techniques are also helpful to reduce calculation time. The objective function of the proposed model is to minimize the total operation time (makespan) which is subject to the mass balance constraints and process boundary conditions. An illustrative case study is presented to demonstrate the features and capabilities of the proposed scheduling system.