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Nowadays, the use of diagnosis-related groups (DRGs) has been increased to claim reimbursement for inpatient care. The overall benefits of using DRGs depend upon the accuracy of clinical coding to obtain reasonable reimbursement. However, the selection of appropriate codes is always challenging and requires professional expertise. The rate of incorrect DRGs is always high due to the heavy workload, poor quality of documentation, and lack of computer assistance. We therefore developed deep learning (DL) models to predict the primary diagnosis for appropriate reimbursement and improving hospital performance. A dataset consisting of 81,486 patients with 128,105 episodes was used for model training and testing. Patients’ age, sex, drugs, diseases, laboratory tests, procedures, and operation history were used as inputs to our multiclass prediction model. Gated recurrent unit (GRU) and artificial neural network (ANN) models were developed to predict 200 primary diagnoses. The performance of the DL models was measured by the area under the receiver operating curve, precision, recall, and F1 score. Of the two DL models, the GRU method, had the best performance in predicting the primary diagnosis (AUC: 0.99, precision: 83.2%, and recall: 66.0%). However, the performance of ANN model for DRGs prediction achieved AUC of 0.99 with a precision of 0.82 and recall of 0.57. The findings of our study show that DL algorithms, especially GRU, can be used to develop DRGs prediction models for identifying primary diagnosis accurately. DeepDRGs would help to claim appropriate financial incentives, enable proper utilization of medical resources, and improve hospital performance.