Electronic health records (EHRs) security is a critical challenge in the implementation and administration of Internet of Medical Things (IoMT) systems within the healthcare sector’s heterogeneous environment. As digital transformation continues to advance, ensuring privacy, integrity, and availability of EHRs become increasingly complex. Various imaging modalities, including PET, MRI, ultrasonography, CT, and X-ray imaging, play vital roles in medical diagnosis, allowing healthcare professionals to visualize and assess the internal structures, functions, and abnormalities within the human body. These diagnostic images are typically stored, shared, and processed for various purposes, including segmentation, feature selection, and image denoising. Cryptography techniques offer a promising solution for protecting sensitive medical image data during storage and transmission. Deep learning has the potential to revolutionize cryptography techniques for securing medical images. This paper explores the application of deep learning techniques in medical image cryptography, aiming to enhance the privacy and security of healthcare data. It investigates the use of deep learning models for image encryption, image resolution enhancement, detection and classification, encrypted compression, key generation, and end-to-end encryption. Finally, we provide insights into the current research challenges and promising directions for future research in the field of deep learning applications in medical image cryptography.