Purpose This study aims to identify health workforce challenges at Iranian hospitals during the COVID-19 pandemic. Design/methodology/approach This was a conventional content analysis study conducted in 2020. The population consisted of the managers (heads of hospitals, managers and matrons) and staff (nurses, physicians, etc.) of eligible hospitals. The participants were selected using purposive sampling, and data saturation was achieved after 28 interviews. The data were analyzed in MAXQDA10. Findings In total, 28 interviews were conducted with 10 women and 18 men. The challenges of hospital human resources were categorized into five main themes and 15 sub-themes. The main themes were the shortage of human resources, burnout, the need to acquire new knowledge and skills, the employees’ health and safety and the reward system. Originality/value Identification of challenges faced by human resources is the first step toward preventing human force shortage and psychological problems in the personnel. Implementing the recommendations of the present study would assist the proper management of hospitals’ human resources.