Background: Hospitals are the most important pillar of the country›s health system, especially when faced with a crisis. One of the most important indicators in evaluating hospitals is performance indicators. This research was done to investigate the effect of the COVID-19 pandemic on the performance indicators of academic and non-academic hospitals in West Azerbaijan province in 2020. Methods: The present cross-sectional descriptive-analytical study was done on all academic and non-academic hospitals of West Azerbaijan province, which examined their performance indicators in 2019 and 2020. The data were analyzed using SPSS 16 software by repeated-measures analysis of variance (ANOVA). Results: The results of repeated-measures ANOVA demonstrated that the effect of time (coronavirus) on the index of bed occupancy ratio was significant (η2=0.24, P=0.006) so that it decreased this index in academic hospitals and had the opposite result in non-academic hospitals. The COVID-19 had a significant effect on the index of average patient stay (η2=0.47, P<0.001) and this index in both types of hospitals increased. Also, the COVID-19 had a significant effect on bed turnover rate (η2=0.32, P=0.001) and it decreased in both types of hospitals. Conclusion: Since academic hospitals are more responsible in dealing with epidemics, it is suggested to pay more attention to their infrastructures. Considering the financial burden of some non-communicable diseases, academic hospitals should be prepared to accept and support them, especially in the early period of the epidemic.