We developed safe and reliable protocol for concurrent intracranial electrical stimulation and functional MRI (es-fMRI) in awake human subjects at 3 T. No adverse effect was observed in our series of 16 subjects who underwent es-fMRI experiment. We compared the es-fMRI effective connectivity with functional connectivity informed by resting-state fMRI and showed both are not redundant and may carries complimentary information about the brain’s connectivity.