Generally, higher education is associated with a reduction in prejudice. However, this effect may differ by gender due to differences in the fields men and women tend to pursue in higher education and the roles higher education plays in attaining social status. The present study explored this possibility in the context of prejudice against Zainichi Koreans (Korean residents in Japan). Unpublished data from an online survey conducted in 2016 were utilized. The final sample consisted of 1,444 Japanese nationals (714 men and 730 women; gender was a dichotomous variable collected via the platform's embedded question), aged 18 to 59 years (M = 36.5, SD = 12.6). Prejudice was assessed using the Zainichi Korean versions of the Modern Racism Scale and the Old-fashioned Racism Scale, as well as the Feeling Thermometer. Educational attainment was collected by five levels and coded into three levels: low (high school or below), medium (junior college, professional training college, etc.), and high (university or above). Multiple regression analyses controlling for age were conducted to examine whether gender moderates the effect of educational attainment. Results indicated a significant interaction of gender and educational attainments only for modern racism. Among men, those with higher education exhibited stronger modern prejudice compared to those with lower education, whereas no such effect was observed among women. The tendency for men to exhibit stronger prejudice was particularly pronounced in the highly educated group, but not in the low and medium-education groups. By contrast, no significant moderation by gender was found for old-fashioned racism or the feeling thermometer. Thus, with respect only to subtle prejudice involving stronger cognitive components (i.e., modern racism), higher education was associated with stronger prejudice among men on contrary to previous findings. Implications of these findings are discussed.