Globally, stroke is a leading cause of death and disability. The classification of motor intentions using brain activity is an important task in the rehabilitation of stroke patients using brain–computer interfaces (BCIs). This paper presents a new method for model training in EEG-based BCI rehabilitation by using overlapping time windows. For this aim, three different models, a convolutional neural network (CNN), graph isomorphism network (GIN), and long short-term memory (LSTM), are used for performing the classification task of motor attempt (MA). We conducted several experiments with different time window lengths, and the results showed that the deep learning approach based on overlapping time windows achieved improvements in classification accuracy, with the LSTM combined vote-counting strategy (VS) having achieved the highest average classification accuracy of 90.3% when the window size was 70. The results verified that the overlapping time window strategy is useful for increasing the efficiency of BCI rehabilitation.