This paper considers a multi-objective model in which operation planning and tool assignment are simultaneously in a Flexible Manufacturing System (FMS). In this regard, the main characteristics of FMS have been analyzed. Then, a comprehensive model, including major system parameters and cost components, has been designed and presented. The proposed model contains cost factors, including machining cost, earliness or tardiness penalties, tool and part movement or switch costs, and idle time costs of tools and machines. Then, a multi-objective model for the problem has been proposed, in which the relative importance of each cost through weighting these costs based on the decision-making goals and the sum of the mentioned costs have been considered simultaneously. Based on the complex nature of the problem, standard solution techniques have yet to be employed. Therefore, to reduce computational times, the Simulated Annealing (SA) algorithm has been used for about 30 minutes (10,000 movements). The total production costs have been decreased from 7,000 to 4333 units using the SA algorithm. Based on the results, a 38% reduction in total production costs has been achieved. Computational results revealed that the proposed method is quite e cient in the multi-objective optimization of FMS within a short computational time.