Scheduling in flexible manufacturing systems (FMSs) may require some complex solutions due to the complexity of the system. In practice, the application of just-in-time (JIT) theory to an FMS has become an attractive research topic, and heuristic scheduling rules are practical methods for scheduling job orders in real-time scheduling. This article presents a model of an FMS, and then applies the JIT theory with some heuristic scheduling rules to the backward scheduling method in particular. We carry out the simulation test for seeking the performance measures obtained by each rule. It is shown that some proposed heuristic scheduling rules give better results than the others. It is also shown that in JIT, the backward scheduling method can be a useful tool in helping the user to select the most suitable rules for the system at hand.