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Posttraumatic stress disorder (PTSD) is a psychiatric disease that may follow traumatic exposure. Current treatments fail in about 30% of patients. Although repeated transcranial magnetic stimulation (rTMS) applied to the prefrontal cortex has been shown to be effective in the treatment of PTSD, the mechanisms need further investigation. Using a PTSD animal model, we verify the beneficial effect of rTMS, and explore the changes it induces on two putative PTSD mechanisms, GABA/glutamate neurotransmission and neuroinflammation. PTSD-like symptoms were elicited in twenty-six mice using a foot-shock conditioning procedure. Fourteen of the 26 were then treated using rTMS (12 were untreated). In the control group (n = 30), 18 were treated with rTMS and 12 were untreated. Animals were sacrificed after re-exposure. The infralimbic (IL) cortex, basolateral amygdala (BLA) and ventral CA1 (vCA1) were isolated using laser microdissection. mRNA was then investigated using PCR array analysis targeting GABA/glutamate and inflammatory pathways. The rTMS treatment significantly decreased the contextual fear memory phenotype. These changes were associated with reduced mRNA expression related to inflammation in the IL cortex and the vCA1, and lowered mRNA-related glutamate neurotransmission and increased GABA neurotransmission in the BLA. Our results suggest that our rTMS treatment was associated with local anti-inflammatory effects and limbic effects, which seemed to counteract PTSD effects. Several of these changes (both stress- and rTMS-induced) have implications for the drug sensitivity of limbic brain areas, and may help in the design of future therapeutic protocols. • rTMS focused on the prefrontal cortex (rTMS-PFC) decreased the fear memory phenotype. • rTMS-PFC was associated with lower infralimbic cortex and ventral CA1 inflammation-related mRNA levels. • rTMS-PFC was associated with higher GABA and lower glutamate neurotransmission-related mRNA in the basolateral amygdala. [ABSTRACT FROM AUTHOR]