This article analyses gender inequalities in educational attainment in the Czech Republic from the novel perspective of multiple educational pathways, which are primary channels of study involving at least two educational transitions (secondary and tertiary) with qualitatively different tracks. We estimate gender gaps in the attainment of six major educational pathways in the Czech Republic across 9 five-year birth cohorts covering the full span of the communist period and the educational expansion of the post-communist period. Our results confirm that gender gaps have increased in recent cohorts, but that these gaps have remained relatively modest in size. The greatest gaps occur in educational pathways involving secondary grammar schools, while gaps involving other tracks of secondary education remain very small. These results suggest that gender gaps in educational attainment in the Czech Republic expose strong gender differences in attendance at secondary grammar schools, in the direction of girls.