We investigated effects of tracking students into higher, more academic, and lower, less academic, school types immediately after primary school (early tracking) instead of having a comprehensive secondary school system (late tracking) on school gender segregation and gender gaps in achievement outcomes. We assumed that, in early tracking countries, girls are more frequently selected into more academic school types, which leads to more school segregation by gender and achievement advantages of girls over boys. In a differences-in-differences design, we compared secondary-school-level gender inequalities between early and late tracking countries, after controlling for primary-school-level differences. We investigated 787 country-by-year observations in 33 matches of primary- and secondary-school-level data sets from three international large-scale assessments. As expected, we found that early tracking increased the degree of school gender segregation. Not conforming to expectations, the evidence did not indicate that tracking had effects on gender gaps in achievement.