Theta burst stimulation (TBS) has been widely used in the treatment of mental disorders, but the cerebral functional difference between intermittent TBS (iTBS) and continuous TBS (cTBS) after one single session of stimulation is not clear. Here we applied resting‐state functional magnetic resonance imaging (RS‐FMRI) to evaluate the alterations in intrinsic brain activity after iTBS and cTBS in the precuneus. We recruited 32 healthy young adults and performed a single session each of iTBS and cTBS at a 1‐week interval. RS‐fMRI was collected at baseline before and immediately after the stimulation. Parameters for regional brain activity (ALFF/fALFF/ReHo) and functional connectivity (FC) with the stimulated site of the precuneus after iTBS and cTBS were calculated and compared between each stimulation using a paired
t
‐test. Correlation analysis among those parameters was calculated to explore whether changes in functional connectivity were associated with local spontaneous activity. After iTBS stimulation, fALFF increased in the bilateral precuneus, while fALFF decreased in the bilateral middle temporal gyrus. Reductions in precuneus FC were found in the bilateral cuneus, superior occipital gyrus, superior temporal gyrus, precentral gyrus, and postcentral gyrus, which correlated with regional activity. After cTBS, fALFF decreased in the bilateral insula, and precuneus FC was decreased in the bilateral inferior occipital gyrus and increased in the thalamus. In the current study, we observed that one session of iTBS or cTBS could cause inhibitory effects in remote brain regions, but only iTBS caused significant local activation in the target region.