In recent years, deep learning has emerged as a powerful tool for developing Brain–Computer Interface (BCI) systems. However, for deep learning models trained entirely on the data from a specific individual, the performance increase has only been marginal owing to the limited availability of subject-specific data. To overcome this, many transfer-based approaches have been proposed, in which deep networks are trained using pre-existing data from other subjects and evaluated on new target subjects. This mode of transfer learning however faces the challenge of substantial inter-subject variability in brain data. Addressing this, in this paper, we propose 5 schemes for adaptation of a deep convolutional neural network (CNN) based electroencephalography (EEG)-BCI system for decoding hand motor imagery (MI). Each scheme fine-tunes an extensively trained, pre-trained model and adapt it to enhance the evaluation performance on a target subject. We report the highest subject-independent performance with an average (N= 54) accuracy of 84.19%(±9. 98%) for two-class motor imagery, while the best accuracy on this dataset is 74.15%(±15. 83%) in the literature. Further, we obtain a statistically significant improvement (p= 0. 005) in classification using the proposed adaptation schemes compared to the baseline subject-independent model.