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Introduction Limited information exists regarding the response of helicopter EMS programs to patients with known or suspected COVID-19. The purpose of this study was to determine changes in flight operations during the early stages of the pandemic. Methods Survey of American College of Emergency Physicians Air Medical Section was conducted between 5/13/2020 and 8/1/2020. COVID-19 prevalence was defined as high vs low based upon cases > 2500 or ≤ 2500. Results Of 48 respondents, the majority (89.6%) reported that their patient guidelines had changed due to COVID-19. 89.6% of programs reported transporting COVID-19 positive patients while 91.5% reported transporting persons under investigation (PUI). The majority of respondents reported additional training in COVID-19 airway management (79.2%) and PPE use (93.6%). Permitted aerosol-generating procedures (AGPs) included BiPAP (40.4%) and high-flow nasal oxygen (66.0%). No difference in guideline changes, positive COVID-19/PUI transport restrictions, or permitted AGPs were noted between high and low prevalence settings. Conclusion COVID-19 has resulted in changes to HEMS guidelines regardless of local disease prevalence. The pandemic has persisted sufficiently long that data regarding the effectiveness of guideline changes should be analyzed. In the absence of definitive data, national best practices should be developed to guide COVID-19 HEMS transport.