Objective: To synthesize the current evidence base concerning the application of Data Envelopment Analysis (DEA) in healthcare efficiency during the COVID-19 pandemic using a scoping review of 13 primary studies. Methods: We consulted databases including Web of Science (WoS) and Scopus, as well as manual search entries up to September 2022. Included studies were primary applications of DEA for assessing healthcare efficiency during the COVID-19 pandemic. Key findings derived from thematic analysis of repeating pattern observations were extracted and tabulated for further synthesis, taking into consideration the variations in DMU definitions, the inclusion of undesirable outputs, the influence of external factors, and the infusion of advanced technologies in DEA. Results: The review observed a diverse application of DMUs, ranging from healthcare supply chains to entire national health systems. There was an evident shift towards incorporating undesirable outputs, such as mortality rates, in the DEA models amidst the pandemic. The influence of external and non-discretionary factors became more pronounced in DEA applications, highlighting the interconnected nature of global health challenges. Notably, several studies integrated advanced computational methods, including machine learning, into traditional DEA, paving the way for enhanced analytical capabilities. Conclusions: DEA, as an efficiency analysis tool, has exhibited adaptability and evolution in its application in the context of the COVID-19 healthcare crisis. By recognizing the multifaceted challenges posed by the pandemic, DEA applications have grown more comprehensive, integrating broader societal and health outcomes. This review provides pivotal insights that can inform policy and healthcare strategies, underscoring the importance of dynamic and comprehensive efficiency analysis methodologies during global health emergencies.