Restless legs syndrome (RLS) is a nocturnal neurological disorder affecting up to 10% of the population. It is characterized by an urge to move and uncomfortable sensations in the legs which can be relieved by movements. Mutations in BTBD9 may confer a higher risk of RLS. We developed Btbd9 knockout mice as an animal model. Functional alterations in the cerebral cortex, especially the sensorimotor cortex, have been found in RLS patients in several imaging studies. However, the role of cerebral cortex in the pathogenesis of RLS remains unclear. To explore this, we used in vivo manganese-enhanced MRI and found that the Btbd9 knockout mice had significantly increased neural activities in the primary somatosensory cortex (S1) and the rostral piriform cortex. Morphometry study revealed a decreased thickness in a part of S1 representing the hindlimb (S1HL) and M1. The electrophysiological recording showed Btbd9 knockout mice had enhanced short-term plasticity at the corticostriatal terminals to D1 medium spiny neurons (MSNs). Furthermore, we specifically knocked out Btbd9 in the cerebral cortex of mice (Btbd9 cKO). The Btbd9 cKO mice showed a rest-phase specific motor restlessness, decreased thermal sensation, and a thinner S1HL and M1. Both Btbd9 knockout and Btbd9 cKO exhibited motor deficits. Our results indicate that systematic BTBD9 deficiency leads to both functional and morphometrical changes of the cerebral cortex, and an alteration in the corticostriatal pathway to D1 MSNs. Loss of BTBD9 only in the cerebral cortex is sufficient to cause similar phenotypes as observed in the Btbd9 complete knockout mice.