Over the last two years, the prolonged massive school closure due to COVID-19 has provoked significant constraints for refugee children. The present study aimed to investigate the perceptions of Greek pre-service teachers on refugee education during the COVID-19 pandemic. A questionnaire was addressed to 32 native university students (n = 32) who attended Education Departments in Western Macedonia in Greece. The results showed that the prevalence of distance education affected pre-service teachers’ perceptions. The access to devices with internet capability as well as the cultural barriers was considered to be crucial factors for the school attendance of refugee children. Participants’ perceptions of the level of teacher preparation in a distance learning environment were related to their level of self-efficacy for supporting refugee students. The findings suggest that in the aftermath of COVID-19 pandemic, the international community should make efforts to ensure the school attendance of all refugee students.