Reduced BDNF and GABAergic inhibition co-occur in neuropsychiatric diseases, including major depression. Genetic rodent studies show a causal link, suggesting the presence of biological pathways that mediate this co-occurrence. Here we show that mice with reduced Bdnf (Bdnf +/-) have upregulated expression of sequestosome-1/p62, an autophagy-associated stress response protein, and reduced surface presentation of α5 subunit-containing GABA A receptor (α5-GABA A R) in prefrontal cortex (PFC) pyramidal neurons. Reducing p62 gene dosage restored α5-GABA A R surface expression and rescued the PFC-relevant behavioral deficits of Bdnf +/mice, including cognitive inflexibility and sensorimotor gating deficits.Increasing p62 levels was sufficient to recreate the molecular and behavioral profiles of Bdnf +/mice. Finally, human postmortem corticolimbic transcriptome analysis suggested reduced autophagic activity in depression. Collectively, the data reveal that autophagy regulation through control of p62 dosage may serve as a mechanism linking reduced BDNF signaling, GABAergic deficits, and psychopathology associated with PFC functional deficits across psychiatric disorders.