Cortical reorganization plays a significant role in recovery of function after injury of the central nervous system. The neural mechanisms that underlie this reorganization may be the same as those normally responsible for skilled behaviors that accompany extended sensory experience and, if better understood, could provide a basis for further promoting recovery of function after injury. The work presented here extends studies of spontaneous cortical reorganization after spinal cord injury to the role of rehabilitative strategies on cortical reorganization. We use a complete spinal transection model to focus on cortical reorganization in response to serotonergic (5-HT) pharmacotherapy without any confounding effects from spared fibers left after partial lesions. 5-HT pharmacotherapy has previously been shown to improve behavioral outcome after SCI but the effect on cortical organization are unknown. After a complete spinal transection in the adult rat, 5-HT pharmacotherapy produced more reorganization in the sensorimotor cortex than would be expected by transection alone. This reorganization was dose dependent, extended into intact (forelimb) motor cortex, and, at least in the hindlimb sensorimotor cortex, followed a somatotopic arrangement. Animals with the greatest behavioral outcome showed the greatest extent of cortical reorganization suggesting that the reorganization is likely to be in response to both direct effects of 5-HT on cortical circuits and indirect effects in response to the behavioral improvement below the level of the lesion.