This study observed the functional changes in brain activity while performing real and imagery movement using functional MRI (fMRI); and to compare the fMRI changes of motor imagery before and after mindfulness meditation (MM) training for correlation with actual brain computer interface (BCI) performance. Thirty-eight participants completed a randomized control trial consisting of 2 groups (MM and non-intervention control groups) to study the effect of MM on BCI performance. The MM group participated in a 4-week MM intervention programme. Out of the 38 cohorts, five participants from the MM group and five from the control group were fMRI scanned for real and imagery movement of right hand, left hand and both feet, before and after intervention. Statistical parametric mapping was used for post processing and analysis of fMRI data. The MM group showed a significant improvement in BCI performance compared to the control group. The fMRI results showed activation of right hand, left hand and both feet motor imagery at fronto-parietal regions before MM training (p <0.05, family wise error). After MM training, the fMRI results revealed a focused activation in 3 out of 4 of the trained subjects during right hand motor imagery, 2 out of 4 of the trained subjects during both feet motor imagery and 1 out of 4 of the trained subjects during left hand motor imagery, compared to the control group. This is also correlated with the improvement of BCI accuracy of the intervention group after MM training. Mindfulness meditation improves BCI performance and is correlated with focused activation of the fronto-parietal region in fMRI during motor imagery.