Previous comparative research has uncovered considerable cross-country differences in occupational gender segregation. There is, however, a lack of research on the role of educational systems in the creation of gender segregation and gendered school-to-work transitions. The aim of this study is to investigate the role of vocational education and the strength of the education–employment linkage in the transmission of horizontal gender segregation from education into the labour market. Transition system literature points to a stronger linkage between education and employment in countries where initial vocational education and training dominates the educational offers, and to a weaker linkage in countries with a stronger focus on general education. Moreover, research on gender segregation in education shows that segregation is especially pronounced in educational systems with a strong vocational education and training sector on the upper secondary level. Based on these insights, we hypothesize that gender segregation in education and its transmission to employment is more pronounced the more distinct a country’s initial vocational education and training system is. To test our assumption, we compare individual school-to-work transitions in Switzerland and Bulgaria, with the vocational principle being more prevalent in the structuring of Swiss educational offers. We use data from the Swiss Youth Panel Survey TREE (N = 3215) and the Bulgarian School Leaver Survey BSLS (N = 885). Following recent developments in multi-group segregation research, entropy-based measurements are calculated to study the school-to-work linkages and the transmission of gender segregation in the two select countries. The empirical results confirm a more pronounced educational gender segregation in Switzerland, which is transferred more strongly into the labour market due to the tighter linkage in that country between education and employment compared to Bulgaria.