The COVID-19 pandemic forced Chinese cross-border students in Hong Kong to participate in online homeschooling for three years while local students attended face-to-face schooling when the situation released. Previous studies have explored the learning challenges or educational inequity among students in online learning during the pandemic. Limited studies explored the educational inequality between local students and cross-border students. To fill this gap, this study explored the extent of educational inequity between Hong Kong local students and Chinese cross-border students. It further investigated the elements that lead to educational inequity between these two groups of students and the long-term consequences of prolonged purely online learning for Chinese cross-border students. This study compared self-regulated learning, perceived academic achievement, and learning challenges between 35 cross-border students and 32 local students in Hong Kong primary schools. According to the questionnaire and open-ended opinion surveys, the findings showed significant evidence of educational inequity between these two groups of students. Through six teachers' semi-structured interviews, the study analyzed students' learning experiences and synthesized the elements contributing to the issue of educational inequity. The study attributed this inequity to infrastructure elements and stakeholder-related elements. Prolonged purely online learning has resulted in negative and positive effects. This study offers practical implications for the government to implement feasible policies to reduce educational inequity in cross-border education and for stakeholders to conduct effective measures to support young learners in the post-COVID world. Lastly, this study discusses the limitations and recommendations for future research. Copyright ©2023 Springer.