This study used off-line repetitive transcranial magnetic stimulation (rTMS) to examine the roles of the superior parietal lobule (SPL) and inferior frontal gyrus (IFG) in a deductive reasoning task. Subjects performed a categorical syllogistic reasoning task involving congruent, incongruent, and abstract trials. Twenty four subjects received magnetic stimulation to the SPL region prior to the task. In the other 24 subjects, TMS was administered to the IFG region before the task. Stimulation lasted for 10min, with an inter-pulse frequency of 1Hz. We found that bilateral SPL (Brodmann area (BA) 7) stimulation disrupted performance on abstract and incongruent reasoning. Left IFG (BA 45) stimulation impaired congruent reasoning performance while paradoxically facilitating incongruent reasoning performance. This resulted in the elimination of the belief-bias. In contrast, right IFG stimulation only impaired incongruent reasoning performance, thus enhancing the belief-bias effect. These findings are largely consistent with the dual-process theory of reasoning, which proposes the existence of two different human reasoning systems: a belief-based heuristic system; and a logic-based analytic system. The present findings suggest that the left language-related IFG (BA 45) may correspond to the heuristic system, while bilateral SPL may underlie the analytic system. The right IFG may play a role in blocking the belief-based heuristic system for solving incongruent reasoning trials. This study could offer an insight about functional roles of distributed brain systems in human deductive reasoning by utilizing the rTMS approach.