This study explores the disparate trajectories of students in Chilean higher education and how these alter socioeconomic segregation within this system. The study follows the cohort of students who entered higher education in 2011 for eight years through census-type data. It uses two segregation indexes to make novel comparisons of socioeconomic segregation at the beginning and the end of their passage through higher education. The results show high dropout rates among students of low socioeconomic status, and high mobility between degree programs and institutions across the socioeconomic spectrum, with significant nuances in the type of mobility experienced by different socioeconomic groups. However, dropouts and transfers between degree programs, institutions, and types of institutions do not significantly modify the levels of socioeconomic segregation seven years after entrance. These results indicate that socioeconomic segregation in higher education is set to a large extent upon entrance to this system.