Previous studies claimed the possible role of the right DLPFC in working memory, usually based on evidence from lesion and imaging studies. In the present study, we explored the role of the right DLPFC in time process, using the repetitive transcranial magnetic stimulation (rTMS) technique. If the right DLPFC indeed plays a role in working memory function during time perception, the change of activity in this region will have more effect on the supra-second intervals which involve working memory function than the sub-second ones. In the first experiment, we explored the role of the right DLPFC in a time reproduction task. The experiment included a baseline condition before rTMS and a post-rTMS condition performed immediately after the cessation of the rTMS train. In each condition, participants need to perform a time reproduction task, which included a time perception and a time reproduction phase. Sixteen undergraduates participated in the rTMS group. Repetitive TMS trains of 10 Hz and 9.5 minutes duration were applied over the right DLPFC of participants. A sham stimuli group (16 participants, without rTMS) was involved to exclude the practice effect and the placebo effect, as well as to test whether the effect of 10 Hz rTMS over the right DLPFC could last to the end of the experiment. To further identify whether the function of the right DLPFC in timing is associated with working memory, we carried out the second experiment with the same rTMS parameters. It is demonstrated that sub-second intervals could be processed depending on the automatic system, while the supra-second intervals were cognitively controlled, involving working memory function. Thus the second experiment was a time discrimination task with sub- and supra-second intervals as standard intervals. Twelve undergraduates participated in the time discrimination task, which consisted of two blocks (short vs. long interval block). The two blocks were counterbalanced between participants. All participants were tested both in baseline and post-rTMS conditions. In the control group, no significant differences were found between the baseline and the post-test condition in the reproduction of both standard intervals; while the duration of 1.5 s was over-estimated in the post-rTMS condition, comparing with the baseline condition. In the discrimination task, the point of subjective equality of 1500 ms duration was smaller in the post-rTMS condition than that of baseline condition; no significant differences between baseline and post-rTMS condition were found in the discrimination of 600 ms. It demonstrated that the right DLPFC played a role in supra-second interval (1500 ms) but not in sub-second interval (600 ms), suggesting it might be involved in the working memory process in the scaler timing theory. To sum up, the estimation of supra-second interval was affected by the application of rTMS over the right DLPFC in both temporal reproduction and discrimination tasks; meanwhile, it did not affect the discrimination of sub-second interval. The results suggested the important role of the right DLPFC in working memory function. No significant differences were found between baseline and post-rTMS condition in the estimation of longer interval (4500 ms), which could be estimated with timing strategy.