This study has compared using fMRI, the changes effected by physiotherapy and yoga in post-stroke recovery. Ischemic stroke patients (n=20) with motor deficits were divided into two groups - yoga and physiotherapy. Each group practiced yoga or physiotherapy for one hour daily for six months, under the supervision of certified yoga trainers and physiotherapists, respectively. Pre- and post- (6 months) intervention evaluations were carried out using fMRI at 3T and NIHSS scores. Results show significant improvement in the NIHSS scores and BOLD activity in the affected sensory motor region of the stroke patients in the yoga group compared to physiotherapy.