Gender difference on spatial visualization has been considered an important factor that impacts the gender gap in academic performance in STEM-related disciplines. The purpose of this meta-analysis was to examine the gender difference on spatial visualization between STEM and non-STEM undergraduate majors. Twenty effect sizes representing STEM majors' spatial ability and 14 effect sizes representing non-STEM majors' spatial ability were included in the present meta-analysis. Results indicated that the overall effect size equalled 0.613 (95% CI = [0.444, 0.782]) in STEM and 0.481 (95% CI = [0.359, 0.604]) in non-STEM. These findings showed that the gender differences on spatial visualization were statistically significant in both STEM and non-STEM majors. The gender difference on spatial visualization in STEM was larger than the gender difference on spatial visualization in non-STEM. In addition, male students' spatial visualization ability was higher than female students' spatial visualization in both STEM and non-STEM majors.