Simultaneous electrical microstimulation (EM) and functional magnetic resonance imaging (fMRI) is a useful tool for probing connectivity across brain areas in vivo. However, it is not clear whether intracortical EM can evoke blood-oxygenation-level-dependent (BOLD) signal in areas connected polysynaptically to the stimulated site. To test for the presence of the BOLD activity evoked by polysynaptic propagation of the EM signal, we conducted simultaneous fMRI and EM in the primary somatosensory cortex (S1) of macaque monkeys. We in fact observed BOLD activations in the contralateral cerebellum which is connected to the stimulation site (i.e. S1) only through polysynaptic pathways. Furthermore, the magnitude of cerebellar activations was dependent on the current amplitude of the EM, confirming the EM is the cause of the cerebellar activations. These results suggest the importance of considering polysynaptic signal propagation, particularly via pathways including subcortical structures, for correctly interpreting 'functional connectivity' as assessed by simultaneous EM and fMRI.