Spinal cord injury may lead to complete or incomplete damage to ascending sensory and/or descending motor pathways and therefore alter neural circuits of the primary motor cortex. Transcranial magnetic stimulation (TMS) is a valuable tool for investigating the function of neural circuitry within primary motor cortex and also for promoting plasticity in these circuits for the ultimate purpose of improving the control of movement. For spinal cord injury, information about motor cortical circuits and TMS approaches to induce plasticity in these circuits is steadily emerging. In this review, we discuss TMS investigations of motor cortical circuitry and review TMS approaches to promote plasticity in motor cortical circuitry in spinal cord injury.