Most of the municipalities in the Gulf region are facing performance related issues in their municipal solid waste management (MSWM) systems. They lack to possess a deliberate inter-municipality benchmarking processes. Instead of identifying the performance gaps for their key components (e.g., personnel productivity, operational reliability, etc.) and adopt proactive measures, the municipalities primarily rely on an efficient emergency response. A novel hierarchical modeling framework, based on deductive reasoning, is developed for performance assessment of MSWM systems. Fuzzy rule based modeling using Simulink-MATLAB was used for performance inferencing at different levels, i.e., component, sub-components, etc. The model is capable of handling the inherent uncertainties due to limited data and imprecise knowledge base. The model’s outcomes can exclusively assist the managers working at different levels of organizational hierarchy for effective decision-making. Performance of the key component, assists the senior management to assess the overall compliance level of performance objectives. Subsequently, operation management can hone in the sub-components to acquire useful information for intra-municipality performance management. While, individual indicators are useful for inter-municipality benchmarking. The model has been implemented on two municipalities operating in Qassim Region, Saudi Arabia. The results demonstrate the model’s pragmatism for continuous performance improvement of MSWM systems in the country and elsewhere.