Cardiovascular Diseases (CVD) and strokes produce immense health and economic burdens globally. Coronary Artery Disease (CAD) is the most common type of cardiovascular disease. Coronary Angiography, which is an invasive treatment, is also the standard procedure for diagnosing CAD. In this work, we illustrate a Medical Decision Support System for the prediction of Coronary Artery Disease (CAD) utilizing Fuzzy Cognitive Maps (FCMs). FCMs are a promising modeling methodology, based on human knowledge, capable of dealing with ambiguity and uncertainty, and learning how to adapt to the unknown or changing environment. The newly proposed MDSS is developed using the basic notions of Fuzzy Logic and Fuzzy Cognitive Maps, with some adjustments to improve the results. The proposed model, tested on a labelled CAD dataset of 303 patients, obtains an accuracy of 78.2% outmatching several state-of-the-art classification algorithms.