Major depression is a prevalent and devastating psychiatric disorder. However, our understanding of the underlying molecular mechanisms is limited. Here, we found reduced expression of zinc finger protein with Krüppel-associated box and SCAN domains 4 (Zkscan4) in the hippocampi of patients with major depressive disorder and stress-susceptible mice. Zkscan4 disruption (Zkscan4-/-) was sufficient to induce depression-like behaviors following subthreshold social stress. Zkscan4 regulated excitatory synaptic transmission mainly through direct interaction with the Htr2a promoter and the recruitment of glucocorticoid receptors for the transcriptional repression of 5-hydroxytryptamine receptor 2a (Htr2a). Reduced excitatory synaptic transmission in the hippocampus and stress susceptibility in Zkscan4-/- mice were restored by pharmacological inhibition, genetic knockdown of Htr2a, or overexpression of the amino-terminal SCAN domain of Zkscan4 (Zkscan41-133) in cornus ammonis region 3. Our findings demonstrate an essential role of Zkscan4 in promoting stress resilience, suggesting a potential antidepressant effect of Zkscan41-133.