The main objective of this study is to generate an optimum solution for capacity planning and appointment scheduling issues, which are frequently encountered in clinical flows with various route and treatment periods at dental hospitals. With this study, given the flow of different existing treatment processes belonging to patients are optimized, and also the continuity of the system is ensured by minimizing the patient waiting times within the existing system. There are many factors which affect the working performance of this designed health system. Regarding hospital management quality, the most important ones of these factors are accurate calculation of appointment capacities, and the assignment of proper staff number at the proper departments with optimum scheduling. These factors were addressed in this study, where the case study implemented at Cukurova University Dental Hospital, the largest dental hospital in Turkey's South Region, were analyzed in detail. It was determined that the system whose performance was designed has developed the most efficient solution. Furthermore, the system modelling was performed by using data received from the real hospital environment and its accuracy was tested by implementation of its effect in the real system. Patient waiting times encountered in the hospital were minimized, and employee productivity was enhanced with this study.