Objective To determine the safety of repetitive transcranial magnetic stimulation (rTMS) on chronic intractable tinnitus. Methods A total of 52 patients diagnosed as chronic intractable tinnitus in our hospital from December 2014 to January 2015 were perspectively enrolled in this study. They were randomly divided into 4 groups, named as groups A to D (n＝13 for each group). They respectively received a 2-week course of active 1Hz rTMS (1 000 or 2 000 pulses), 5 Hz rTMS (500 or 1 000 pulses) to the left temporoparietal cortex region, 5 times/week. The measurements of pure tone auditory and motor cortex evoked potential were taken before and immediately after the end of the interventions. Results There was no significant difference in pure tone audiometry threshold in the 4 groups before and after the interventions. A slight decrease was seen in the motor cortex threshold, but with no significant difference. One patient was attacked with dizziness, one case experienced headache, and one patient had aggravated tinnitus, but which all disappeared or was alleviated at the next day after stopping treatment. No injury at the site of stimulation or epileptic seizure was seen in the whole course of treatment. Conclusion rTMS is safe and reliable in the suppression of tinnitus, and could be widely applied in clinical practice.