Prior research has shown that the two writing systems of the Japanese orthography are processed differently: kana (syllabic symbols) are processed like other phonetic languages such as English, while kanji (a logographic writing system) are processed like other logographic languages such as Chinese. Previous work done with the Stroop task in Japanese has shown that these differences in processing strategies create differences in Stroop effects. This study investigated the Stroop effect in kana and kanji using functional magnetic resonance imaging (fMRI) to examine the similarities and differences in brain processing between logographic and phonetic languages. Nine native Japanese speakers performed the Stroop task in both kana and kanji scripts during fMRI. Both scripts individually produced significant Stroop effects as measured by the behavioral reaction time data. The imaging data for both scripts showed brain activation in the anterior cingulate gyrus, an area involved in inhibiting automatic processing. Though behavioral data showed no significant differences between the Stroop effects in kana and kanji, there were differential areas of activation in fMRI found for each writing system. In fMRI, the Stroop task activated an area in the left inferior parietal lobule during the kana task and the left inferior frontal gyrus during the kanji task. The results of the present study suggest that the Stroop task in Japanese kana and kanji elicits differential activation in brain regions involved in conflict detection and resolution for syllabic and logographic writing systems.