In an FMS, a most complicated problem to be solved may be the scheduling problem which is flexible due to the complexity of the system. FMS needs very high cost for installation, therefore in order to get high efficiency, the most appropriate schedule (in general means the schedule with the minimum cost) should be obtained in the stage of scheduling. In this article an FMS model which is a flow shop-type production system has been engaged. Scheduling method is based on the multiple objectives and the total objective function is to minimize the value of all concerned objectives. Consequently, scheduling algorithm has been composed by applying the backward scheduling with Simulated Annealing (SA) method to realize JIT theory. Finally, numerical example has been conducted to show how the scheduling algorithm works and especially to find the efficiency of the proposed algorithm. According to the numerical example, it is shown that the algorithm works well when it was applied with the concerned FMS system.