Myocarditis is the form of an inflammation of the middle layer of the heart wall which is caused by a viral infection and can affect the heart muscle and its electrical system. It has remained as one of the most challenging diagnoses in cardiology. Myocardial is the prime cause of unexpected death in approximately 20% of adults less than 40 years of age. Cardiac MRI (CMR) has been considered as a noninvasive and golden standard diagnostic tool for suspected myocarditis and plays an indispensable role in diagnosing various cardiac diseases. However, the performance of CMR is heavily dependent on the clinical presentation and non-specific features such as chest pain, arrhythmia, and heart failure. Besides, other imaging factors like artifacts, technical errors, pulse sequence, acquisition parameters, contrast agent dose, and more importantly qualitatively visual interpretation can affect the result of the diagnosis. This paper introduces a new deep learning-based model called Convolutional Neural Network-Clustering (CNN-KCL) to diagnose the Myocarditis. The hybrid CNN-KCL method performs the early and accurate diagnosis of Myocarditis. To the best-of-our-knowledge, a Convolutional neural network has never been used before for the diagnosis of Myocarditis. In this study, we used 47 subjects to diagnose myocarditis patients from Tehran's Omid Hospital. The total number of data examined is 10425. Our results demonstrate that CNN-KCL achieves 92.3% in terms of diagnosis myocarditis prediction accuracy which is significantly better than those reported in previous studies.