•Tissue signals bordering tumor are valuable in predicting tumor prognosis.•Post-treatment images are of great significance for prognosis prediction.•Assessing images of tumor after each treatment course is a possible prospect.•The post-treatment images predict the prognosis better than pre-treatment images do. We aimed to predict the prognosis of advanced nasopharyngeal carcinoma (stage Ⅲ-Ⅳa) using Pre- and Post-treatment MR images based on deep learning (DL). A total of 206 patients with primary nasopharyngeal carcinoma who were diagnosed and treated at the Renmin Hospital of Wuhan University between June 2012 and January 2018 were retrospectively selected. A rectangular region of interest (ROI), which included the tumor area, surrounding tissues and organs, was delineated on each Pre- and Post-treatment MR image. Two Inception-Resnet-V2 based transfer learning models, named Pre-model and Post-model, were trained with the Pre-treatment images and the Post-treatment images, respectively. In addition, an ensemble learning model based on the Pre-model and Post-models was established. The three established models were evaluated by receiver operating characteristic curve (ROC), confusion matrix, and Harrell's concordance indices (C-index). High-risk-related gradient-weighted class activation mapping (Grad-CAM) images were developed according to the DL models. The Pre-model, Post-model, and ensemble model displayed a C-index of 0.717 (95% CI: 0.639 to 0.795), 0.811 (95% CI: 0.745–0.877), 0.830 (95% CI: 0.767–0.893), and AUC of 0.741 (95% CI: 0.584–0.900), 0.806 (95% CI: 0.670–0.942), and 0.842 (95% CI: 0.718–0.967) for the test cohort, respectively. In comparison with the models, the performance of Post-model was better than the performance of Pre-model, which indicated the importance of Post-treatment images for prognosis prediction. All three DL models performed better than the TNM staging system (0.723, 95% CI: 0.567–0.879). The captured features presented on Grad-CAM images suggested that the areas around the tumor and lymph nodes were related to the prognosis of the tumor. The three established DL models based on Pre- and Post-treatment MR images have a better performance than TNM staging. Post-treatment MR images are of great significance for prognosis prediction and could contribute to clinical decision-making.