Objectives: Repetitive transcranial magnetic stimulation (rTMS) can modulate neuronal circuits and also enhance spinal cord plasticity. Our aim of this study was to delineate the effect of rTMS on the functional recovery of upper extremity in patients with incomplete spinal cord injury, especially central cord syndrome (CCS), and detect the changes of spinal cord tracts crossing the lesion by diffusion tensor imaging (DTI). Method: Fourteen patients with CCS,which level of injury was between C4 to C6, were performed rTMS with high frequency (20Hz) over the unilateral motor cortex for 5 days as well as the conventional occupational therapy. The non-treated side of each subject was used as control. We assessed the neurological status using International Standard for Neuro- logical Classification of Spinal Cord Injury (ISNCSCI), and functional status of upper extremities using the Jebsen hand function and O'conner finger dexterity tests twice; before treatment, and 1 month after treatment. DTI was performed on the injured cervical spinal cord, obtained fractional anisotrophy (FA), apparent diffusion coefficient (ADC) at each level, and calculate imaginary spinal cord tracts of each subject. Results: The neurological status of the upper extremity motor score in the treated side using ISNCSCI was improved in all subjects otherwise only 10 of 14 subjects (71.4%) showed some improvements of non-treated side at 1 month after treatment. The functional status including the writing score of Jebsen hand function test were also significantly improved more in treated side in comparison with non-treated side at 1 month. The FA values and the number of imaginary spinal cord tracts of treated side at the injured level were also increased more than those of non-treated side in the same subjects. Any side effects such as seizure, severe headache, nausea or vision problem was not observed during rTMS treatment and follow-up period. Conclusions: The high frequency rTMS was effective to improve the neurological and functional status of CCS patients and might increase the spinal cord plasticity without any serious side effects.