Intermittent theta burst stimulation (iTBS), a specialized protocol of repetitive transcranial magnetic stimulation (rTMS), is a non-invasive method used to study brain function in health and disease in both animal models and humans. Despite increasing interest, fundamental questions regarding the cellular and molecular effects of iTBS/rTMS on brain activity remain unanswered. It is generally recognized that c-Fos can be used as a molecular marker of neuronal activity following different types of stimuli. Therefore, this study aimed to investigate the effects of seven-day iTBS application on c-Fos expression in various brain regions of healthy, 2.5-month old male Wistar rats. We investigated how subchronic iTBS affects c-Fos expression in various brain regions and explored its impact on locomotion and exploratory behavior using the Open Field Test. Our findings revealed increased c-Fos levels in the prelimbic cortex and slightly in the dentate gyrus with iTBS compared to sham treatment. However, there was no significant difference in c-Fos levels in the CA3 region of the hippocampus, retrosplenial cortex, and brainstem between iTBS and sham groups. Despite regional effects on c-Fos expression, iTBS did not alter locomotion or exploratory behavior. These data suggest that the iTBS protocol might induce different neuronal activities depending on the brain region and thus influence different brain functions. This study was supported by the Ministry of Science, Technological Development and Innovation, Republic of Serbia grants No. 451-03-65/2024-03/ 200178 and 451-03-66/2024-03/ 200178.