This paper illustrates a prototype for a Clinical Decision Support System (CDSS), using Supervised Machine Learning (SML) to derive rules from pre-constructed cases or to automatically generate rules. We propose an integrated architecture invoking two main components - Rule Pattern Matching Process (RPMP) and Auto Rule Generation Process (ARGP). The RPMP searches for and matches rules from a clinically derived reference set, successful discovery resulting in continued processing through the system. If no rule is found, the AGRP is automatically activated. The AGRP has been designed based on the SML approach. A Decision Tree Algorithm has been used and nested If-else statements applied to transform the decision tree algorithm to generate rules. For experimental purposes, we have developed a prototype and implemented a learning algorithm for generating auto rules for the diagnosis of Acute Rheumatic Fever (ARF). Based on results, the prototype can successfully generate the auto rules for ARF diagnosis. The prototype was designed to classify the ARF stages into “Detected”, “Suspected” and “Not detected”, in addition, it has classifiers capable of classifying the severity levels of detected stage into Severe, Moderate or Mild case. We simulated a set of 104 cases of ARF and observed the rules. The prototype successfully generated the new rule and classified it with the appropriate category (stage). In summary, the applied approach performed extremely well and the developed prototype provided reliable rules for ARF diagnosis. This prototype therefore reduces the task of manually creating ARF diagnosis rules. This approach could be applied in other clinical diagnosis processes.