Autism Spectrum Disorder (ASD) is characterized by early onset of behavioural and cognitive alterations. Low plasma levels of oxytocin have also been found in ASD patients and recently, a critical role for the enzyme CD38 in the regulation of oxytocin release was demonstrated. CD38 is important in regulating several Ca2+ dependent pathways, but beyond its role in regulating oxytocin secretion, it is not known whether a deficit in CD38 expression leads to functional modifications of the prefrontal cortex, a structure involved in social behaviour. Here, we report that CD38-/- male mice show an abnormal cortex development, an excitation-inhibition balance shifted towards a higher excitation, and impaired synaptic plasticity in the prefrontal cortex such as those observed in various mouse models of ASD. We also show that a lack of CD38 alters social behaviour and emotional responses. Finally, examining neuromodulators known to control behavioural flexibility, we found elevated monoamine levels in the prefrontal cortex of CD38-/- adult mice. Overall our study unveiled major changes in prefrontal cortex physiological mechanisms and provides new evidence that the CD38-/- mouse could be a relevant model to study pathophysiological brain mechanisms of mental disorders such as ASD.