•Reconfiguring nearby FMC of the failure node can increase the resilience of FMS.•Increasing the storage capacity can further improve the resilience of FMS.•Two theorems can significantly reduce the cardinality of the strategy set. In the past few years, due to various man-made and natural disasters such as COVID-19, the manufacturing industry worldwide has undergone significant changes. To counter and prevent the losses, it is important to consider the resilience of the manufacturing systems. In this paper, a new method for designing resilient Flexible Manufacturing System (FMS) is presented. The FMS is modeled by a directional network. The method consists of two types of strategies: one is to use Flexible Manufacturing Cells (FMC) and reconfigure route (Strategy A) and the other is to use a combination of FMC and its extended storage capacity (Strategy B). The resilience is measured by the Production Lost and the Investment Return. Using the Monte Carlo Simulation, FMS can be investigated under various failure conditions. For complex FMS, the size of the strategy set is very large. Thus, two theorems are proposed to reduce the size without effecting the optimal solution. A demonstration example with 33 nodes fabricating 5 kinds of products is presented. It shows that compared to simply waiting for fixing failure, the use of Strategy A and Strategy B will result in more than 10% increase in Investment Return.