The treatment plan of colorectal neoplasm differs based on histology. Although new endoscopic imaging systems have been developed, there are clear diagnostic thresholds and requirements in using them. To overcome these limitations, we trained convolutional neural networks (CNNs) with endoscopic images and developed a computer-aided diagnostic (CAD) system which predicts the pathologic histology of colorectal adenoma. We retrospectively collected colonoscopic images from two tertiary hospitals and labeled 3400 images into one of 4 classes according to the final histology: normal, low-grade dysplasia, high-grade dysplasia, and adenocarcinoma. We implemented a CAD system based on ensemble learning with three CNN models which transfer the knowledge learned from common digital photography images to the colonoscopic image domain. The deep learning models were trained to classify the colorectal adenoma into these 4 classes. We compared the outcomes of the CNN models to those of two endoscopist groups having different years of experience, and visualized the model predictions using Class Activation Mapping. In our multi-center study, our CNN-CAD system identified the histology of colorectal adenoma with as sensitivity 77.25%, specificity of 92.42%, positive predictive value of 77.16%, negative predictive value of 92.58% averaged over the 4 classes, and mean diagnostic time of 0.12 s per image. Our experiments demonstrate that the CNN-CAD showed a similar performance to that of endoscopic experts and outperformed that of trainees. The model visualization results also showed reasonable regions of interest to explain the classification decisions of CAD systems. We suggest that CNN-CAD system can predict the histology of colorectal adenoma.