PurposeThis paper investigates the overall system risk for a foodgrains supply chain capturing the interrelationship among the risk factors and the effect of risk mitigation strategies.Design/methodology/approachThis paper first calculates the weight of risk factors using an integrated approach of failure mode, effects analysis and fuzzy VIKOR technique. Next, the weights are utilized as input for the weighted fuzzy Petri-net (WFPN) approach to calculate the system risk.FindingsTwo different WFPN models are developed based on the relationships among the risk factors, and both models demonstrate a higher risk value for the overall system.Originality/valueThe proposed methodology will help practitioners or managers understand the complexity involved in the system by capturing the interrelationship behaviour. This study also considers the concurrent effect of risk mitigation strategies for calculating the overall system risk, which helps to improve the system’s performance.