Purpose: The purpose of this study was to determine the effect of direct functional magnetic stimulation (FMS) of affected spinal cord on motor recovery following spinal cord injury in rats. Methods: After a contusion injury at the spinal level T9 using an NYU Impactor, functional magnetic stimulation was delivered by a magnetic stimulator through a round prototype coil (7 cm in diameter). Stimulation parameters were set as follows: repetition rate = 50 Hz (stimulus intensity 100% = 0.18 T), stimulation time = 20 min. Functional magnetic stimulation was administered twice a day, 5 days per week for 8 weeks starting 4 days after spinal cord injury. Functional magnetic stimulationwas delivered directly to the affected spinal cord. Outcomes of locomotor performance were assessed by the Basso Beattie Bresnahan (BBB) locomotor rating scale and by an inclined plane test weekly for 8 weeks. Results: In the BBB test, hindlimb motor function in the Functional magnetic stimulation group improved significantly more compared to the control group at 3, 4, 6, 7, and 8 weeks (p<0.05). In the inclined plane test, the angle of the plane in the functional magnetic stimulation group increased significantly more compared to the control group at 4, 5, 7, and 8 weeks (p<0.05). Conclusion: Our results demonstrate that direct Functional magnetic stimulation of the lesional site may have beneficial effects on motor improvement after spinal cord injury.