A scheduling problem in a flexible manufacturing system (FMS) is considered to be a composite of two interdependent tasks: loading and sequencing. Formulations are presented for the loading problem with two objectives: (i) minimization of the system workload unbalance, and (ii) minimization of system unbalance and the number of late jobs; including constraints such as the number of tools slots with duplications, unique job routing, nonsplitting of jobs and machine capacity. For both the objectives, heuristic methods are developed and performance is compared with the exact mixed integer programming solutions. A simulation model is developed for investigating the system performance for the problem of minimizing the system unbalance using heuristic and sequential loading methods in conjunction with four—FIFO, SPT, LPT and MOPR—dispatching rules.