Background: The COVID-19 pandemic affected school students in several ways, including mental health issues, physical activity, or education. The objective of this paper is to shed light on an underexplored aspect of the pandemic by estimating its impact on the provision and utilization of routine school-based medical services by school doctors in Austria. Methods: We utilize survey-based data on school medical services collected by the Austrian Ministry of Education, Science and Research in the 2018/2019 and 2019/2020 school years. We compare both years using fixed-effects regression. Results: In the 2019/20 school year, compared to 2018/19, we observe a decline in engagement of school health professionals in health-promoting school projects (-4.3%-points) and in first-aid training sessions (-8.6%-points). Most networking activities with other school-based advisory teams decreased; only membership of a school-based crisis team increased (+6.9%-points). The share of compulsory check-ups (-24.8%-points) and student-initiated medical consultations (-17.7%-points) decreased significantly. Implications for School Health Policy, Practice, and Equity: Findings outline the need for strategies to provide school-based medical services in crises, especially in countries where school health professionals are key points of contact for medical concerns. Conclusions: Our results indicate a significant reduction in routine school medical services during the pandemic.