Background and objectiveThe COVID-19 pandemic placed considerable pressure on the health care systems and caused many disruptions to the care hospital system around the globe. This study aimed to analyze the performance of hospitals affiliated with the University of Medical Sciences and Health Services of South Khorasan Province before and during COVID-19.MethodThis cross-sectional study tracked the financial performance (FP) and service performance (SP) of 12 hospitals affiliated with South Khorasan University of Medical Sciences and Health Services using the Farabar system and Hospital Information System (HIS). Our study covered two time periods: from February 2018 to February 2020 (pre-COVID-19) and from February 2020 to February 2021 (during COVID-19). SP analysis of hospitals was performed by examining the trend of monthly changes before and during the COVID-19 pandemic and analyzed using SPSS software version 22 and Paired Sample T-Test. FP of hospitals was analyzed through relevant ratios and analyzed using Microsoft Office Excel.ResultsMost SP indicators decreased considerably in all hospitals during COVID-19. FP ratios (e.g., activity and leverage ratios) increased during either or both pre-COVID or COVID periods. Compared to before COVID-19, the operating margin ratio and operating expenses coverage from operating income increased from -0.50 and 66.55 to -1.42 and 41.32, respectively, during COVID-19. Moreover, the net profit margin ratio and Return On Assets (ROA) ratio were increased during COVID-19.ConclusionCOVID-19 has decreased the FP and SP of hospitals due to limitations in providing services to patients since the beginning of COVID-19. Measures such as providing various financing resources and improving the financial resilience of hospitals are essential. Funds should be disbursed to offset hospitals’ losses due to reduced elective and outpatient revenue. Policymakers should come up with holistic policies to tackle the adverse impact of such crises in the future, support hospitals financially, and consider allocating additional funding to them during emergencies.