While the number of international students attending UK universities has been increasing in recent years, the 2021/22 and 2022/23 academic years saw a decline in applications from EU-domiciled students. However, the extent and varying impact of this decline remain to be estimated and disentangled from the impacts of the COVID-19 pandemic. Using difference-in-differences (DID) in a hierarchical regression framework and Universities and Colleges Admissions Service (UCAS) data, we aim to quantify the decline in the number of student applications post-Brexit. We find evidence of an overall decline of 65% in the 2021 academic year in successful applications from EU students as a result of Brexit. This decline is more pronounced for non-Russell Group institutions, as well as for Health and Life Sciences and Arts and Languages. Furthermore, we explore the spatial heterogeneity of the impact of Brexit across EU countries of origin, observing the greatest effects for Poland and Germany, though this varies depending on institution type and subject. We also show that higher rates of COVID-19 stringency in the country of origin led to greater applications for UK higher education institutions. Our results are important for government and institutional policymakers seeking to understand where losses occur and how international students respond to external shocks and policy changes. Our study quantifies the distinct impacts of Brexit and COVID-19 and offers valuable insights to guide strategic interventions to sustain the UK’s attractiveness as a destination for international students.