The Covid-19 pandemic has given rise to broad challenges in the air transportation sector by leading to the closure of borders and imposing restrictive measures taken immediately. At the same time, Brazil struggled to contain and better prepare to deal with the consequences of the pandemic. Given the context, this work aims to analyze the impact of Covid-19 on the efficiency of air transportation sector and evaluating the prospects of its recovery compared to the prepandemic level. The present study makes use of Data Envelopment Analysis methodology seeking to identify the technical efficiency of both passenger and cargo flights. The methodology was applied by adopting relevant input and output indicators. We confirmed the negative impacts on the sector suffered from the pandemic. Cargo flights in Brazilian domestic market experienced a larger loss than passenger flights. Moreover, the study shows the Brazilian market did not perform ideally to prevent impacts of the second wave of Covid-19. For governments and policy makers, they need to carefully consider the effects of policies to be implemented. Our research also provides decision-making factors to organizations and companies related to business performance.