Mutations in autism-associated gene Shank3 have been associated to alterations in striatal function and core autistic behaviors. However, the neocortical substrates affected by Shank3 mutations remain undetermined. By using structural and functional MRI in Shank3B mutant mice, we identified key alterations in prefrontal and associative regions of the mouse default mode network (DMN). Specifically, we show that prefrontal and antero-posterior areas of the DMN present decreased gray matter volume, an effect associated with reduced local and long-range prefrontal functional connectivity. Our findings suggest that Shank3 mutations may predispose to autism via a selective trophic and functional downregulation of prefrontal areas.