Since the underlying mechanisms of neurorehabilitation are not fully understood, the prognosis of stroke recovery faces significant difficulties. Recovery outcomes can vary when undergoing different treatments; however, few models have been developed to predict patient outcomes toward multiple treatments. In this study, we aimed to investigate the potential of predicting a treatment's outcome using a deep learning prognosis model developed for another treatment. A total of 15 stroke survivors were recruited in this study, and their clinical and physiological data were measured before and after the treatment (clinical measurement, biomechanical measurement, and electroencephalography (EEG) measurement). Multiple biomarkers and clinical scale scores of patients who had completed manual stretching rehabilitation training were analyzed. Data were used to train deep learning prognosis models, yielding an 87.50% prognosis accuracy. Pre-trained prognosis models were then applied to patients who completed robotic-assisted stretching training, yielding a prognosis accuracy of 91.84%. Interpretation of the deep learning models revealed several key factors influencing patients' recoveries, including the plantar-flexor active range of movement (r = 0.930, P = 0.02), dorsiflexor strength (r = 0.932, P = 0.002), plantar-flexor strength (r = 0.930, P = 0.002), EEG power spectrum density and EEG functional connectivities in the occipital, central parietal, and parietal areas. Our results suggest (i) that deep learning can be a promising method for accurate prediction of the recovery potential of stroke patients in clinical scenarios and (ii) that it can be successfully applied to different rehabilitation trainings with explainable factors.