Stroke is one of endangering disease if not treated properly and could lean to death. Most people unwilling to check their health because of high cost, lack of medical service, medical staff of neurologist and their limited working time. Therefore, we need an expert system that can help in early diagnosis of stroke. The Dempster Shafer and Certainty Factor methods are expert systems methods used in many cases to support uncertainty from the expert. The aim of this study is to compare two methods to determine the best method in the expert system for diagnosing stroke, by calculating symptoms so as to produce CF values in the Certainty Factor method and density values in the Dempster Shafer method. The data used in the study to diagnose stroke consisted of data on eighteen disease symptoms and two types of stroke identified. Based on the results of testing on 105 test data, the accuracy value of the expert system for diagnosing stroke using the Dempster Shafer method is 95.2% and the accuracy value of the expert system for diagnosing stroke with the Certainty factor method is 98.1%.