Intellectual and social disabilities are common comorbidities in adolescents and adults with MAGEL2 gene deficiency characterizing the Prader-Willi and Schaaf-Yang neurodevelopmental syndromes. The cellular and molecular mechanisms underlying the risk for autism in these syndromes are not understood. We ask whether vasopressin functions are altered by MAGEL2 deficiency and whether a treatment with vasopressin can alleviate the disabilities of social behavior. We used Magel2 knockout mice (adult males) combined with optogenetic or pharmacological tools to characterize disease modifications in the vasopressinergic brain system and monitor its impact on neurophysiological and behavioral functions. We find that the activation of vasopressin neurons and its projections in the lateral septum are inappropriate to perform a social habituation/discrimination task. Mechanistically, the lack of vasopressin impedes the deactivation of somatostatin neurons in the lateral septum, which predicts social discrimination deficits. Correction of vasopressin septal content by administration or optogenetic stimulation of projecting axons suppressed the activity of somatostatin neurons and ameliorated social behavior. This preclinical study identifies vasopressin in the lateral septum as a key factor in the pathophysiology.