Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive neuromodulation technique used to treat many neuropsychiatric conditions. However, the mechanisms underlying its mode of action are still unclear. This is the first rodent study using resting-state fMRI to examine low-intensity (LI) rTMS effects, in an effort to provide a direct means of comparison between rodent and human studies. Our study shows that similar to human rTMS, 10 Hz LI- rTMS alters the resting brain activity of rats directly at the site of stimulation (e.g. cortex) as well as in remote but inter-connected brain regions (e.g. hippocampus).