Brain-computer interface (BCI) technology has the potential as a post-stroke rehabilitation tool, and the efficacy of the technology is most often demonstrated through output peripherals such as robots, orthosis and computers. In this study, the EEG signals recorded during the course of upper limb stroke rehabilitaion using motor imagery BCI were analyzed to better understand the effect of BCI therapy for post-stroke rehabilitation. The stroke patients recruited underwent 10 sessions of 1-hour BCI with robotic feedback for 2 weeks, 5 times a week. The analysis was performed by computing the coherences of the EEG in the lesion and contralesion side of the hemisphere from each session, and the coherence index of the lesion hemisphere (0 ≤ CI ≤ 1) was computed. The coherence index represents the rate of activation of the lesion hemisphere, and the correlation with the Fugl-Meyer assessment (FMA) before and after the BCI therapy was investigated. Significant improvement in the FMA scores was reported for five of the six patients (p = 0.01). The analysis showed that the number of sessions with CI ≥ 0.5 correlated with the change in the FMA scores. This suggests that post-stroke motor recovery best results from the activation in the lesion hemisphere, which is in agreement with previous studies performed using multimodal imaging technologies.