Diabetic retinopathy (DR) is a disease that forms as a complication of diabetes. It is particularly dangerous since it often goes unnoticed and can lead to blindness if not detected early. Despite the clear importance and urgency of such an illness, there is no precise system for the early detection of DR so far. Fortunately, such system could be achieved using deep learning including convolutional neural networks (CNNs), which gained momentum in the field of medical imaging due to its capability of being effectively integrated into various systems in a manner that significantly improves the performance. This project proposes a computer aided diagnostic (CAD) system for the early detection of non-proliferative DR (NPDR) using CNNs. The proposed system is developed for the optical coherence tomography (OCT) imaging modality. Throughout this paper, all aspects of deployment of the proposed system are studied starting from the preprocessing stage required to extract input retina patches to train the CNN without resizing the image, to the use of transfer learning principals and how to effectively combine features in order to optimize performance. This is done through investigating several scenarios for the system setup and then selecting the best one, which from the results revealed to be a two pre-trained CNNs based system, in which one of these CNNs is independently fed by nasal retina patches and the other one by temporal retina patches. The proposed transfer learning based CAD system achieves a promising accuracy of 94%.  This project is implemented with MATLAB software.