Stroke is the second foremost cause of death worldwide and is one of the most common causes of disability. Several approaches have been proposed to manage stroke patient rehabilitation such as robotic devices and virtual reality systems, and researchers have found that the brain-computer interfaces (BCI) approaches can provide better results. Therefore, the most challenging tasks with BCI applications involve identifying the best technique(s) that can reveal the neuron stimulus information from the patients’ brains and extracting the most effective features from these signals as well. Accordingly, the main novelty of this paper is twofold: propose a new feature fusion method for motor imagery (MI)-based BCI and develop an automatic MI framework to detect the changes pre- and post-rehabilitation. This study investigated the electroencephalography (EEG) dataset from post-stroke patients with upper extremity hemiparesis. All patients performed 25 MI-based BCI sessions with follow up assessment visits to examine the functional changes before and after EEG neurorehabilitation. In the first stage, conventional filters and automatic independent component analysis with wavelet transform (AICA-WT) denoising technique were used. Next, attributes from time, entropy and frequency domains were computed, and the effective features were combined into time–entropy–frequency (TEF) attributes. Consequently, the AICA-WT and the TEF fusion set were utilised to develop an AICA-WT-TEF framework. Then, support vector machine (SVM), k-nearest neighbours (kNN) and random forest (RF) classification technique were tested for MI-based BCI rehabilitation. The proposed AICA-WT-TEF framework with RF classifier achieves the best results compared with other classifiers. Finally, the proposed framework and feature fusion set achieve a significant performance in terms of accuracy measures compared to the state-of-the-art. Therefore, the proposed methods could be crucial for improving the process of automatic MI rehabilitation and are recommended for implementation in real-time applications.