ABSTRACT Deep learning methods have proved a promising performance for electroencephalography-based brain-computer interfaces (EEG-BCI). It is particularly encouraging that a subject-independent model can be trained using a large amount of other subjects’ data. Transfer learning methods such as adaptation or fine-tuning can be used on the pre-trained model to improve the performance. This study examined the influence of fine-tuning on the subject-independent model for EEG-based motor imagery (MI) classification using a genetic algorithm (GA). The proposed method is evaluated on the binary class MI dataset from the Korea University EEG dataset. Results show that the proposed GA-based fine-tuning approach statistically improved the average classification accuracy of the baseline model from 84.46% to 87.29%. More interestingly, our approach shows significant improvement in cases where the performance of the baseline model is poor after fine-tuning using other approaches. Further, layer-wise relevance propagation (LRP) is used to analyze the adapted models to gain a deeper understanding of the neurophysiological explanations underlying the model’s decision.