The diagnosis of multiple sclerosis (MS) is difficult considering its complexity, variety in signs and symptoms, and its similarity to the signs and symptoms of other neurological diseases. The purpose of this study is to design and develop a clinical decision support system (CDSS) to help physicians diagnose MS with a relapsing-remitting phenotype. The CDSS software was developed in four stages: requirement analysis, system design, system development, and system evaluation. The Rational Rose and SQL Server were used to design the object-oriented conceptual model and develop the database. The C sharp programming language and the Visual Studio programming environment were used to develop the software. To evaluate the efficiency and applicability of the software, the data of 130 medical records of patients aged 20 to 40 between 2017 and 2019 were used along with the Nilsson standard questionnaire. SPSS Statistics was also used to analyze the data. For MS diagnosis, CDSS had a sensitivity, specificity and accuracy of 1, 0.97 and 0.99, respectively, and the area under the ROC curve was 0.98. The agreement rate of kappa coefficient (κ) between software diagnosis and physician’s diagnosis was 0.98. The average score of software users was 98.33%, 96.65%, and 96.9% regarding the ease of learning, memorability, and satisfaction, respectively. Therefore, the applicability of the CDSS for MS diagnosis was confirmed by the neurologists. The evaluation findings show that CDSS can help physicians in the accurate and timely diagnosis of MS by using the rule-based method.