Few prospective studies have investigated the etiology of brain tumor, especially among Asian populations. Both coffee and green tea are popular beverages, but their relation with brain tumor risk, particularly with glioma, has been inconsistent in epidemiological studies. In this study, we evaluated the association between coffee and greed tea intake and brain tumor risk in a Japanese population. We evaluated a cohort of 106,324 subjects (50,438 men and 55,886 women) in the Japan Public Health Center‐Based Prospective Study (JPHC Study). Subjects were followed from 1990 for Cohort I and 1993 for Cohort II until December 31, 2012. One hundred and fifty‐seven (70 men and 87 women) newly diagnosed cases of brain tumor were identified during the study period. Hazard ratio (HR) and 95% confidence intervals (95%CIs) for the association between coffee or green tea consumption and brain tumor risk were assessed using a Cox proportional hazards regression model. We found a significant inverse association between coffee consumption and brain tumor risk in both total subjects (≥3 cups/day; HR = 0.47, 95%CI = 0.22–0.98) and in women (≥3 cups/day; HR = 0.24, 95%CI = 0.06–0.99), although the number of cases in the highest category was small. Furthermore, glioma risk tended to decrease with higher coffee consumption (≥3 cups/day; HR = 0.54, 95%CI = 0.16–1.80). No association was seen between green tea and brain tumor risk. In conclusion, our study suggested that coffee consumption might reduce the risk of brain tumor, including that of glioma, in the Japanese population. What's new? How do coffee and green tea affect risk of brain tumor? Previous studies have yielded conflicting results. In this paper, the authors investigated the effects of both beverages in a Japanese population. They collected data from more than 100,000 subjects enrolled in the Japanese Public Health Center‐Based Prospective Study covering a period of 22 years. Their analysis suggests that drinking more than three cups of coffee per day reduced risk of brain tumor, including glioma—although few participants drank that much coffee. Green tea consumption, they found, did not affect brain cancer risk.