In this study, we investigated the effect of the dynamic changes in brain activation during neurofeedback training in the classification of the different brain states associated with the target tasks. We hypothesized that ongoing activation patterns could change during neurofeedback session due to learning effects and, in the process, could affect the performance of brain state classifiers trained using data obtained prior to the session. Using a motor imagery paradigm, we then examined the application of an incremental training approach where classifiers were continuously updated in order to account for these activation changes. Our results confirmed our hypothesis that neurofeedback training could be associated with dynamic changes in brain activation characterized by an initially more widespread brain activation followed by a more focused and localized activation pattern. By continuously updating the trained classifiers after each feedback run, significant improvement in accurately classifying the different brain states associated with the target motor imagery tasks was achieved. These findings suggest the importance of taking into account brain activation changes during neurofeedback in order to provide more reliable and accurate feedback information to the participants, which is critical for an effective neurofeedback application.