Background and purpose Activation of indoleamine 2,3-dioxygenase (IDO) in prefrontal cortex (PFC) is closely related to depression. It has been proved that prelimbic (PrL) and infralimbic (IL) regions of medial PFC are involved in emotion regulation, and may play distinct roles in regulation of depression. However, the mechanism of how IDO in PrL or IL affects depressive behaviors remains unclear. Experimental approach IDO inhibitor 1-MT was directly injected into PrL and IL of depressive rats induced by ICV-STZ, respectively. Depressive- and anxiety-behaviors were evaluated in forced swim test, sucrose preference test, novelty-suppressed feeding test, novel object recognition test and open field test. HPLC‒MS/MS detected kynurenine metabolites, ELISA detected cytokines, Western blot examined protein expression and Golgi staining assessed synaptic plasticity. Immunofluorescence staining was used to observe the expression and morphology of glial cells. Key results Dissimilar abnormalities were observed in PrL and IL of ICV-STZ depressed rats. In PrL, astrocyte defects were manifested, including reduced GFAP-positive cells, glial transporters and kynurenic acid, and morphological damage. In IL, microglial overactivation was manifested by increased cytokines, Iba1-positive cells and 3-hydroxy-kynurenine, accompanied by morphological alterations. Meanwhile, synaptic plasticity was decreased in both subregions. Microinjection of 1-MT at PrL or IL may improve depressive behaviors by reversing these different abnormalities in PrL and IL, respectively, without influencing anxiety behavior. Conclusions and implications Overall, the antidepressant effects of 1-MT by inhibiting IDO in PrL or IL are realized through different pathways, that is, by enhancing neuroprotective effects in PrL and attenuating neurotoxic response in IL.