Hypertrophic cardiomyopathy (HCM) can lead to serious cardiac problems. HCM is often diagnosed by an expert using cardiovascular magnetic resonance (CMR) images obtained from patients. In this research, we aimed to develop a deep learning technique to automate HCM diagnosis. CMR images of 37421 healthy and 21846 HCM patients were obtained during two years. Images obtained from female patients form 53% of the collected dataset. The mean and standard deviation of the dataset patients’ age are 48.2 and 19.5 years, respectively. Three experts inspected images and determined whether a case has HCM or not. New data augmentation was used to generate new images by employing color filtering on the existing ones. To classify the augmented images, we used a deep convolutional neural network (CNN). To the best of our knowledge, this is the first time CNN is used for HCM diagnosis. We designed our CNN from scratch to reach acceptable diagnosis accuracy. Comparing the designed algorithm output with the experts’ opinions, the method could achieve accuracy of 95.23%, recall of 97.90%, and specificity of 93.06% on the original dataset. The same performance metrics for the designed algorithm on the augmented dataset were 98.53%, 98.70%, and 95.21%, respectively. We have also experimented with different optimizers (e.g. Adadelta and Adagrad) and other data augmentation methods (e.g. height shift and rotation) to further evaluate the proposed method. Using our data augmentation method, accuracy of 98.53% were achieved which is higher than the best accuracy (95.83%) obtained by the other data augmentation methods which have been evaluated. The upper bound on difference between true error rate and empirical error rate of the proposed method has also been provided in order to present better performance analysis. The advantages of employing the proposed method are elimination of contrast agent and its complications, decreased CMR examination time, lower costs for patients and cardiac imaging centers.