This study empirically examines the impact of the COVID-19 pandemic on university students’ enrollment behaviors using a comprehensive database of university enrollments from 2012 to 2022. Our analysis reveals a 3.7% decline in the probability of re-enrollment for the subsequent academic year among the first cohort affected by the pandemic. This effect is particularly pronounced among students entering university, as well as among non-free lunch students, international students, and male students. The medium-term analysis indicates that the pandemic led to a significant shift in enrollment behaviors, decreasing the likelihood of enrolling in subsequent years and reducing graduation rates two years after the pandemic. Moreover, we find that exposure to stricter lockdown policies led to a 3.8% decrease in enrollment behaviors. We investigate three potential mechanisms: (i) exposure to the pandemic, (ii) labor market opportunities, and (iii) university quality. However, we find little evidence to support that these factors are significantly associated with changes in enrollment behaviors. These findings contribute to our understanding of the disruptive consequences of the COVID-19 pandemic on students’ educational trajectories and highlight its lasting impact on enrollment behaviors.