This paper presents a decision support system (DSS) modeled by a fuzzy expert system (FES) for medical diagnosis to help physicians make better decisions. The proposed system collects comprehensive information about a disease from a group of experts. To this aim, a cross-sectional study is conducted by asking physicians’ expertise on all symptoms relevant to a disease. A fuzzy rule based system is then formed based on this information, which contains a set of significant symptoms relevant to the suspected disease. Linguistic fuzzy values are assigned to model each symptom. The input of the system is the severity level of each symptom reported by patients. The proposed FES considers two approaches to account for uncertain inputs from patients. Two case studies on kidney stone and kidney infection were conducted to demonstrate how the proposed method could be used. A group of patients were used to validate the effectiveness of the proposed expert system. The results show that the proposed fuzzy expert system is capable of diagnosing diseases with a high degree of accuracy and precision comparing to a couple of machine learning methods.