In this study we investigated the effect of 2 weeks of robot-aided virtual reality therapy for the paretic upper limb in stroke patients on changes in brain activation. Brain activation was acquired during the resting state and during visually-guided hand movement. fMRI analysis focused on characterizing functional connectivity with ipsilesional primary motor cortex (iM1) at rest and during execution of paretic hand movement. Two subjects who sustained a stroke more than 6 months ago participated. Before and after the training period, motor function was evaluated (Wolf Motor Function Test [WMFT], Jebsen Test of Hand Function [JTHF]). After the training period, clinical outcomes (WMFT and JTHF) improved in both subjects. The resting state functional connectivity (rsFC) maps and task-related functional connectivity with iM1 showed different magnitudes of activation, however, the general directionality of the pattern (increases versus decreases) was similar. Specifically, both the rsFC and the task-related functional connectivity between iM1 and contralesional primary motor cortex (cM1) decreased after the therapy for the first subject and increased for the second subject. Our preliminary data suggest that resting state functional connectivity may be a useful measure of brain reorganization, particularly for subjects with limited volitional control of the paretic limb.