Introduction Due to the vital importance of early diagnosis and intervention of congenital hearing loss, the aim of this study was to compare the rate of newborn hearing screening before and after the COVID-19 pandemic quarantine. Materials and methods In this study, the data related to 6144 newborns during two 18-month time periods before and after the onset of the COVID-19 pandemic quarantine, was analyzed. Results From all visited newborns, 3770 and 2374 referred to the centre before and after the COVID-19 pandemic quarantine, respectively. There were statistically significant differences in the results of screening and the referral rate of neonates before and after the pandemic (p = 0.00). The results showed that both the residents of urban and rural regions visited for newborn hearing screening less frequently after the onset of the pandemic, but no statistically significant difference was shown between the number of boys and girls before and after the pandemic (p = 0.72). Conclusion Our results help gain new insights regarding the impacts of disruptive events such as pandemics on the implementation of health screening programs. Boosting public knowledge by providing families with proper education appears to be helpful in preventing the negative effects of delayed implementation of health screening programs.