Currently, robotic manufacturing cells entail complex decisions concerning sequencing issues due to uncertainty which arises in different parameters such as time to failure, time to repair and cycle times that can be effectively supported by computer simulation models. The paper focused on part sequencing of a two-machine robotic cell in a flow shop which produces different parts. The process is supported by a single gripper robot to load/unload products and also in displacement within the system. This study considers machine failures and repair such that S2 cycle time and total production cost should be minimized. In this study, simulation facilitated input part sequence and also data envelopment analysis method is applied to trace the optimum sequence for satisfying the objective functions. Results through some numerical examples showed some simulation advantages specially to model many uncertainties and what if analysis.