Depression is the leading contributor to disability and suicide ideation. Informed by the insights from bioinformatics analyses, this study investigates the roles of E2F transcription factor 2 (E2F2) and protein tyrosine phosphatase non-receptor type 6 (PTPN6) in the activation of microglia and the manifestation of depressive-like behavior in mice. Chronic unpredictable mild stress was applied to induce a mouse model of depression, while a cellular model featuring microglia was established through exposure to lipopolysaccharide and adenosine triphosphate. E2F2 was upregulated whereas PTPN6 was downregulated in these models. Notably, E2F2 was found to bind to the PTPN6 promoter, thereby repressing its transcription. Various behavioral tests demonstrated that silencing of E2F2, accomplished via shRNA transfection, led to increased locomotor activity, heightened social interaction rates, enhanced sucrose preference, and reduced immobility time in response to stress stimuli in mice. Furthermore, E2F2 silencing effectively reduced expression of Iba1, a microglial activation marker, and decreased concentrations of pro-inflammatory cytokines both in vivo and in vitro. However, these mitigating effects were countered by additional PTPN6 silencing. In conclusion, this study investigation underscores the role of E2F2 in promoting inflammatory activation of microglia and exacerbating depressive-like behavior in mice by repressing PTPN6 transcription.