Background: The topic of gender differences in mathematical performance has received considerable attention in the fields of education, sociology, economics and psychology. Aims: We analysed gender differences based on data from the Beijing Assessment of Educational Quality in China. Sample: A large data set of Grade 5 and Grade 8 students who took the mathematical test from 2008 to 2013 (n = 73,318) were analysed. Method: Meta-analysis was used in this research. Results: The findings were as follows. (1) No gender differences in mathematical achievement exist among students in Grade 5, relatively small gender differences exist in Grade 8, females scored higher than males, and variance of male students is larger than that of females in both Grade 5 and Grade 8. (2) Except for statistics and probability, gender differences in other domains in Grade 8 are significantly higher than those in Grade 5, and female students outperform males. (3) The ratio of students of both gender in Grade 5 and Grade 8 at the 95-100% percentile level shows no significant differences. However, the ratio of male students is significantly higher than that of females at the 0-5% percentile level. (4) In Grade 5, the extent to which females outperformed males in low SES group is larger than that in higher SES groups, and in Grade 8, the magnitude of gender differences in urban schools is smaller than that in rural schools. Conclusion: There is a small gender difference among the 8th graders, with the male disadvantage at the bottom of the distribution. And gender differences also vary across school locations.