Background Pregnant women are one of the most vulnerable groups in the Covid-19 pandemic. Due to the lack of knowledge about fetal and perinatal complications following Covid-19 infection, the association of Covid-19 pandemic and congenital anomalies in babies conceived and born during this pandemic is unclear. Current study aimed to investigate the association between the Covid-19 pandemic and congenital birth anomalies in Iran. The population of newborns whose embryonic period coincided with the Covid-19 crises were compared with a similar group born during the pre-Covid-19 period. Methods This is a retrospective comparative analysis of congenital birth anomalies in Iran; desired data was extracted from national birth registry database. All registered congenital anomalies in hospital births were compared between two time periods: During Covid-19 (1st November 2020- 28th February 2021) and Before Covid-19 (1st November 2019-29th February 2020). Incidence of congenital anomalies at birth were compared and analyzed between these two time periods. Results The incidence of congenital birth anomalies are significantly increased during Covid-19 pandemic compared with before Covid-19 (P value < 0.00001). The number of all types of anomalies has increased in the current pandemic, but the congenital anomalies of the central nervous system (P value = 0.04) and Genitourinary (P value = 0.03) have a larger contribution than before. Conclusion Covid-19 pandemic are associated with congenital anomalies at birth. There are several factors in the Covid-19 pandemic which can affect fetal development in the first trimester of pregnancy. Possible reasons include vertical transmission of Covid-19 infection; maternal fever, stress and anxiety; insufficient preconception and prenatal care; neglect of fetal screening; and poverty imposed by this pandemic.