A transformer-based deep learning model, MR-Transformer, was developed for total knee replacement (TKR) prediction using magnetic resonance imaging (MRI). The model incorporates the ImageNet pre-training and captures three-dimensional (3D) spatial correlation from the MR images. The performance of the proposed model was compared to existing state-of-the-art deep learning models for knee injury diagnosis using MRI. Knee MR scans of four different tissue contrasts from the Osteoarthritis Initiative and Multicenter Osteoarthritis Study databases were utilized in the study. Experimental results demonstrated the state-of-the-art performance of the proposed model on TKR prediction using MRI.