The continuous growth of the population causes an increased demand for our healthcare services. Insufficient hospitals face challenges to serve the patient within a preferable duration. Long lines in front of counters increase the processing time of a patient. From the entry to the completion, plenty of time waste just for unscheduled hospital management system. Job shop scheduling is an optimization process in which jobs are assigned with maintain a particular sequence. In this paper, we proposed flexible job shop scheduling to solve this type of problem by considering patients as job and test counter as machine for the optimization of the processing time and increase the efficiency of a hospital or a clinic. Genetic Algorithm was used to analyze the processing time for multiple counter of a hospital for a stable and effective scheduling. The results showed that an optimized make-span was generated and patients could fulfill their needs much quickly after applying flexible job shop scheduling.