Gender disparity in education is a perpetually compelling issue. It is especially attention-grabbing in economically disadvantaged areas, as it may reinforce backwardness on top of economic vulnerability. Underpinned by the self-determination theory, this study examined the underlying mechanisms that gave rise to gender differences in the academic achievement of upper primary grades students from disadvantaged areas of China. We drew on a dataset of 5,032 students in grades four through six, assembled from 89 schools in three disadvantaged counties spanning two provinces. The results showed that girls significantly outperformed boys in Chinese and English across three grades. Unexpectedly, boys performed statistically identical to girls in math, where boys had generally been considered more adept. Personality explained the gender differences, while the mediating effects of student-teacher relationships were only found in the girls' group. The findings emphasized the importance of increasing supportive efforts to address the boy's academic risks.