BackgroundDuring the covid-19 pandemic, hospitals have faced several challenges, so they need to identify and address effective management strategies to cope with these challenges that enhance their current knowledge to deal with similar challenges in the future. This study aimed to identify managerial strategies for dealing with Covid-19 pandemic challenges at a hospital in southeastern Iran.MethodsThis qualitative content analysis study used purposive sampling to select eight managers, three nurses, and one worker from Shahid Bahonar Hospital. In this study, semi-structured interviews were used to collect data and Lundman and Graneheim’s approach was used to analyze them.ResultsThree hundred fifty codes remained after constant comparison, compression, and merging. The results demonstrated one theme “Managerial reengineering in the healthcare system during the Covid-19 crisis”, two main categories, seven subcategories and, 19 sub- subcategories. The first main category was “The difficulty of managing challenges,“ including “Insufficient resources and physical space”, “Socio-organizational challenges” and, “Incompetence and unpreparedness of managers.“ The second main category was “Reforming the management duties.“ This category included “Planning and decision-making,“ “Organization,“ “Leadership and motivation,“ and “Monitoring and control.”ConclusionsHospitals and managers were less prepared to cope with the Covid-19 crisis challenges due to health system organizations’ less attention to biological crises. Healthcare organizations can carefully evaluate these challenges, and the strategies managers adopt to deal with these problems. They also can identify the strategies’ strengths and weaknesses and propose more effective strategies. As a result, healthcare organizations will be better prepared for similar crises.