Research shows a heterogeneous picture of migration-related disparities regarding adolescents’ educational trajectories at the end of lower-secondary education. Among other disparities, migrants face large disadvantages with regard to the transition to vocational education and training (VET). They are, however, also more likely to change to upper-secondary school tracks at the end of lower-secondary education. Using longitudinal data drawn from the German National Educational Panel Study (NEPS, Starting Cohort 4), this study empirically captures patterns in school-leavers’ transition trajectories after lower-secondary education and empirically tests theoretical mechanisms of migration-related educational inequalities. Building on the concept of secondary effects of migrant origin, this study asks to what extent self-selection explains migration-related disparities in the educational trajectories at the end of lower-secondary education. Particular attention is devoted to the extent to which migration-related inequalities in adolescents’ transitions can be explained by differences in (1) rational choice factors and (2) the educational expectations and demands of parents and friends. The results show that rational choice factors and the educational expectations of social groups largely contribute to migration-related educational inequalities. The results provide important starting points for educational policy discussions on strategies and measures to address migration-related inequalities in the transition to VET.