Functional magnetic resonance imaging (fMRI) under deep brain stimulation (DBS) provides important insights into understanding the connection of the neural networks. However, such research has been limited by incompatibility of common electrode in the MR environment. To address such issue, we fabricated a novel graphene based neural microelectrode, which exhibited excellent charge storage capacity and MRI compatibility. Using such microelectrode, we successfully demonstrate deep brain stimulation of subthalamic nucleus (STN) evoked robust BOLD activation in cortex and basal ganglia nucleus of the Parkinsonian rats with minimal image artifact. Therefore, MR-compatible graphene microelectrode could provide unique opportunity for simultaneous DBS-fMRI studies.