This paper was the first to analyze the magnitude, temporal evolution, and decomposition of socioeconomic segregation in Chilean higher education, over the period 2009 to 2017, in which relevant policies aimed at strengthening inclusion and equity in the system were introduced. Two segregation indices, the dissimilarity index and the square root index, are used to meet these objectives. The results show high and persistent segregation for high socioeconomic status students, in contrast to the moderate and decreasing segregation levels seen in the low and middle socioeconomic groups. Besides, the decomposition exercise posits the universities as the focus of segregation in this system, where both the institution and the degree program constitute relevant factors in understanding the unequal distribution of high socioeconomic status students. These results invite an in-depth look at the mechanisms that hinder social integration in this area, with a particular emphasis on the segregation of the highest socioeconomic status students, whose place in this system promotes their academic and social differentiation.