Key points To shed light on the controversial issue of how chronic immobilization affects cortical output, adult rats were subjected to intracortical microstimulation at different time‐points during and after unilateral forelimb casting. After cast application, cortical hypoexcitability appeared bilateral, specific for forelimb area, but stronger in the contralateral‐to‐cast hemisphere. Cortical excitability progressively decreased over 30 days of immobilization and, after cast removal, steadily increased, but remained partial at 15 days. Cortical application of the GABAA‐receptor antagonist bicuculline revealed an impairment of intracortical synaptic connectivity in the forelimb area during the cast period and for up to 15 days after cast removal. Rehabilitation using a rotarod performance protocol did not advance the normalization of normal forelimb map extension and enabled cortical output towards the distal forelimb only in sites that had maintained their excitability. Cortical hypoexcitability following immobilization is caused by reversible impairment of intracortical synaptic connectivity. This may suggest new approaches in conditions that require longterm limb immobilization. Abstract Experimental and clinical studies have attempted to evaluate the changes in cortical activity seen after immobilization‐induced longterm sensorimotor restriction, although results remain controversial. We used intracortical microstimulation (ICMS), which provides topographic movement representations of the motor areas in both hemispheres with optimal spatial characterization, combined with behavioural testing to unravel the effects of limb immobilization on movement representations in the rat primary motor cortex (M1). Unilateral forelimb immobilization in rats was achieved by casting the entire limb and leaving the cast in place for 15 or 30 days. Changes in M1 were bilateral and specific for the forelimb area, but were stronger in the contralateral‐to‐cast hemisphere. The threshold current required to evoke forelimb movement increased progressively over the period in cast, whereas the forelimb area size decreased and the non‐excitable area size increased. Casting resulted in a redistribution of proximal/distal movement representations: proximal forelimb representation increased, whereas distal representation decreased in size. ICMS after cast removal showed a reversal of changes, which remained partial at 15 days. Local application of the GABAA‐antagonist bicuculline revealed the impairment of cortical synaptic connectivity in the forelimb area during the period of cast and for up to 15 days after cast removal. Six days of rehabilitation using a rotarod performance protocol after cast removal did not advance map size normalization in the contralateral‐to‐cast M1 and enabled the cortical output towards the distal forelimb only in sites that had maintained their excitability. These results are relevant to our understanding of adult M1 plasticity during and after sensorimotor deprivation, and to new approaches to conditions that require longterm limb immobilization.