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• Automatically predict treatment response using MRI. • Accurately identify the complete response that can avoid surgical resection. • Easily adapted to other imaging data for outcome prediction. Accurate outcome prediction prior to treatment can facilitate trial design and clinical decision making to achieve better treatment outcome. We developed the DeepTOP tool with deep learning approach for region-of-interest segmentation and clinical outcome prediction using magnetic resonance imaging (MRI). DeepTOP was constructed with an automatic pipeline from tumor segmentation to outcome prediction. In DeepTOP, the segmentation model used U-Net with a codec structure, and the prediction model was built with a three-layer convolutional neural network. In addition, the weight distribution algorithm was developed and applied in the prediction model to optimize the performance of DeepTOP. A total of 1889 MRI slices from 99 patients in the phase III multicenter randomized clinical trial (NCT01211210) on neoadjuvant treatment for rectal cancer was used to train and validate DeepTOP. We systematically optimized and validated DeepTOP with multiple devised pipelines in the clinical trial, demonstrating a better performance than other competitive algorithms in accurate tumor segmentation (Dice coefficient: 0.79; IoU: 0.75; slice-specific sensitivity: 0.98) and predicting pathological complete response to chemo/radiotherapy (accuracy: 0.789; specificity: 0.725; and sensitivity: 0.812). DeepTOP is a deep learning tool that could avoid manual labeling and feature extraction and realize automatic tumor segmentation and treatment outcome prediction by using the original MRI images. DeepTOP is open to provide a tractable framework for the development of other segmentation and predicting tools in clinical settings. DeepTOP-based tumor assessment can provide a reference for clinical decision making and facilitate imaging marker-driven trial design. [ABSTRACT FROM AUTHOR]