In the research on life-course outcomes, there is a long-standing debate on the relative importance of institutional structure and human agency. This study examines how structure and agency influence educational trajectories in Switzerland. The Swiss education system is hierarchically differentiated but permeable, providing both standard and non-standard pathways to higher education. Using data from a 15-year panel survey, the study assesses, first, the extent to which lower-secondary-school track attendance is associated with individuals’ probability of moving into an academic or vocational programme at upper-secondary level and, second, how this predicts the probability of subsequently entering a university. The study also examines how human agency influences these probabilities. Results of a structural equation model show that lower-secondary track attendance significantly predicts individuals’ probability of transitioning into academic education, whereas human agency plays a minor, albeit non-negligible, role in this regard. In turn, pursuing an academic rather than a vocational programme is associated with a 47-percentage point (or 16-fold) higher probability of subsequently attending university. Individuals comparatively rarely follow non-standard pathways to university, irrespective of their level of agency. The education system channels educational trajectories, but the power of the channelling effect varies across the different junctures of the system.