Increasing regulatory demands are forcing the pharmaceutical industry to invest its available resources carefully. This is especially challenging for small- and middle-sized companies. Computer simulation software like FlexSim allows one to explore variations in production processes without the need to interrupt the running process. Here, we applied a discrete-event simulation to two approved film-coated tablet production processes. The simulations were performed with FlexSim (FlexSim Deutschland—Ingenieurbüro für Simulationsdienstleistung Ralf Gruber, Kirchlengern, Germany). Process visualization was done using Cmap Tools (Florida Institute for Human and Machine Cognition, Pensacola, FL, USA), and statistical analysis used MiniTab® (Minitab GmbH, Munich, Germany). The most critical elements identified during model building were the model logic, operating schedule, and processing times. These factors were graphically and statistically verified. To optimize the utilization of employees, three different shift systems were simulated, thereby revealing the advantages of two-shift and one-and-a-half-shift systems compared to a one-shift system. Without the need to interrupt any currently running production processes, we found that changing the shift system could save 50–53% of the campaign duration and 9–14% of the labor costs. In summary, we demonstrated that FlexSim, which is mainly used in logistics, can also be advantageously implemented for modeling and optimizing pharmaceutical production processes.