The article deals with the structural conflict between academic and vocational postcompulsory secondary education involving the negative selection to vocational education. The conflict is treated from the historical perspective with the aim of explaining historical factors and social mechanisms that have contributed to the persistence of the conflict to the present day. The theoretical framework combines neoinstitutionalism and historical sociology. We argue that the historical developmental path of the education system has played a significant role in the emergence of the above-mentioned structural conflict, and the principal mechanism of institutional persistence lies with cultural-cognitive institutions. As a result of systematic historical path analysis, we can conclude that Khrushchev's educational reform in the 1960s instigated a pattern of negative selection to vocational education that has persisted despite radical societal changes related to the post-Soviet transition. However, not only historically evolved understandings but also the interactions between them and actual labour market outcomes of vocational education seem to function as the main reinforcing mechanisms.