Abstract Content-based image retrieval (CBIR) is a technique used to retrieve image from an image database. However, the CBIR process suffers from less accuracy to retrieve many images from an extensive image database and prove the privacy of images. The aim of this article is to address the issues of accuracy utilizing deep learning techniques such as the CNN method. Also, it provides the necessary privacy for images using fully homomorphic encryption methods by Cheon–Kim–Kim–Song (CKKS). The system has been proposed, namely RCNN_CKKS, which includes two parts. The first part (offline processing) extracts automated high-level features based on a flatting layer in a convolutional neural network (CNN) and then stores these features in a new dataset. In the second part (online processing), the client sends the encrypted image to the server, which depends on the CNN model trained to extract features of the sent image. Next, the extracted features are compared with the stored features using a Hamming distance method to retrieve all similar images. Finally, the server encrypts all retrieved images and sends them to the client. Deep-learning results on plain images were 97.87% for classification and 98.94% for retriever images. At the same time, the NIST test was used to check the security of CKKS when applied to Canadian Institute for Advanced Research (CIFAR-10) dataset. Through these results, researchers conclude that deep learning is an effective method for image retrieval and that a CKKS method is appropriate for image privacy protection.