Stroke survivors have access to a wide range of drug and non-drug treatments for the resulting physiological and functional problems. However, comprehensive therapies typically fail to meet the demands of a large percentage of patients. The recent clinical studies to improve protocol scientific evidence have resulted in a new development phase for rehabilitation medicine. Stroke rehabilitation supports individuals to lead a normal life. It assists the physicians in offering an effective environment to the patients. The evaluation of a patient’s progress in rehabilitation is based on the clinician’s subjective observations and the patient’s self-reported data. Deep learning techniques offer novel forms of individualized treatment. Nonetheless, missing data is one of the crucial factors that reduces the performance of data classification techniques. Thus, there is a demand for functional recovery prediction models for supporting stroke patients (SPs) to improve their quality of life. In this study, the researchers intend to build a framework for predicting functional outcomes using the electronic health record data of SPs. An attention-based bidirectional gated recurrent unit is used for developing the data imputation model. In addition, a shallow-convolutional neural network is employed for predicting the functional outcomes based on the modified Barthel Index. Data from 356 SPs were utilized for evaluating the performance of the proposed framework with the benchmark metrics and baseline models. The findings reveal that the proposed framework outperforms the state-of-the-art classification by achieving an average accuracy, precision, recall, F1-measure, specificity, and sensitivity of 98.18, 97.48, 98, 97.74, 96.74, and 97.24, respectively. The proposed framework can be implemented in real time to support SPs.