Predicting gait recovery after a spinal cord injury (SCI) during an acute rehabilitation phase is important for planning rehabilitation strategies. However, few studies have been conducted on this topic to date. In this study, we developed a deep learning-based prediction model for gait recovery after SCI upon discharge from an acute rehabilitation facility. Data were collected from 405 patients with acute SCI admitted to the acute rehabilitation facility of Korea University Anam Hospital between June 2008 and December 2022. The dependent variable was Functional Ambulation Category at the time of discharge (FAC-DC). Seventy-one independent variables were selected from the existing literature: basic information, International Standards for Neurological Classification of SCI scores, neurogenic bladders, initial FAC, and somatosensory-evoked potentials of the lower extremity. Recurrent neural network (RNN), linear regression (LR), Ridge, and Lasso methods were compared for FAC-DC prediction in terms of the root-mean-squared error (RMSE). RNN variable importance, which is the RMSE gap between a complete RNN model and an RNN model excluding a certain variable, was used to evaluate the contribution of this variable. Based on the results of this study, the performance of the RNN was far better than that of LR, Ridge, and Lasso. The respective RMSEs were 0.3738, 2.2831, 1.3161, and 1.0246 for all the participants; 0.3727, 1.7176, 1.3914, and 1.3524 for those with trauma; and 0.3728, 1.7516, 1.1012, and 0.8889 for those without trauma. In terms of RNN variable importance, lower-extremity motor strength (right and left ankle dorsiflexors, right knee extensors, and left long toe extensors) and the neurological level of injury were ranked among the top five across the boards. Therefore, initial FAC was the seventh, third, and ninth most important predictor for all participants, those with trauma, and those without trauma, respectively. In conclusion, this study developed a deep learning-based prediction model with excellent performance for gait recovery after SCI at the time of discharge from an acute rehabilitation facility. This study also demonstrated the strength of deep learning as an explainable artificial intelligence method for identifying the most important predictors.