School based health centers (SBHCs) are often at the front line of medical and mental health services for students in the schools they serve. Citywide school closures in New York City in March 2020 and ongoing social distancing procedures resulted in significant changes in SBHC services as well as access to these services. Furthermore, the combination of COVID-19 related stressors and the increased likelihood of adverse childhood events experienced by urban youth creates conditions for the exacerbation of mental health concerns among youth in metropolitan areas. The following article will explore the role of SBHCs as community agents focused on prevention and reduction of mental health concerns prior and during the current pandemic, as well as existing health disparities experienced by urban youth populations. The authors will also discuss research examining mental health concerns already present in global populations affected by COVID-19 as it may foreshadow the challenges to be faced by U.S. urban youth. Lastly, the authors describe recommendations, practice implications, and opportunities for preventative strategies and therapeutic interventions in school based health settings.