Flexible manufacturing systems (FMS) are production systems consisting of identical multipurpose numerically controlled machines (workstations), automated material handling system, tools, loading and unloading stations, inspection stations, storage areas and a hierarchical control system. Job sequencing and routing are fundamental components of FMS A flexible manufacturing system (FMS) is a manufacturing system in which there is some flexibility that allows the system to react in the case of changes. Scheduling of an FMS is very complicated, particularly in dynamic environment. A simulation based FMS scheduling system can take into account these uncertainties and perform accordingly. Fuzzy logic based simulation is easy to apply and can consider a number variables with reasonable amount of accuracy. Here the proposed model will prioritize the job and select the best alternative route with multi-criteria scheduling through an approach based on a fuzzy logic. There are three criteria for both the job sequencing and routing with 27 rules. With the help of the rules the sequence of the jobs are done and the best route is selected.