Re-operations and revisions are often performed in patients who have undergone total shoulder arthroplasty (TSA) and reverse total shoulder arthroplasty (RTSA). This necessitates an accurate recognition of the implant model and manufacturer to set the correct apparatus and procedure according to the patient’s anatomy as personalized medicine. Owing to unavailability and ambiguity in the medical data of a patient, expert surgeons identify the implants through a visual comparison of X-ray images. False steps cause heedlessness, morbidity, extra monetary weight, and a waste of time. Despite significant advancements in pattern recognition and deep learning in the medical field, extremely limited research has been conducted on classifying shoulder implants. To overcome these problems, we propose a robust deep learning-based framework comprised of an ensemble of convolutional neural networks (CNNs) to classify shoulder implants in X-ray images of different patients. Through our rotational invariant augmentation, the size of the training dataset is increased 36-fold. The modified ResNet and DenseNet are then combined deeply to form a dense residual ensemble-network (DRE-Net). To evaluate DRE-Net, experiments were executed on a 10-fold cross-validation on the openly available shoulder implant X-ray dataset. The experimental results showed that DRE-Net achieved an accuracy, F1-score, precision, and recall of 85.92%, 84.69%, 85.33%, and 84.11%, respectively, which were higher than those of the state-of-the-art methods. Moreover, we confirmed the generalization capability of our network by testing it in an open-world configuration, and the effectiveness of rotational invariant augmentation.