In March 2020, the World Health Organization declared a COVID-19 pandemic. The aim of this study was to compare the causes of and statistics on neonatal mortality in Russia in 2020 and 2019 using the Rosstat A-5 forms that aggregate data from perinatal death certificates. In 2020, there was a 7.6% reduction in the absolute number of live births relative to 2019. In 2020, the overall early neonatal death rate (1.59‰) fell by 4.4% in comparison with 2019 (1.67‰). However, neonatal mortality in the Southern and Far Eastern Federal Districts rose by 20.5% and 6.1%, respectively. Respiratory diseases were the most common cause of early neonatal mortality across Russia (37.3% and 40.2% relative to the total number of neonatal deaths in 2019 and 2020, respectively). Congenital sepsis accounted for 43.6% and 46.6% of early neonatal deaths from infectious diseases and for 7.3% and 7.9% of all early neonatal deaths reported in 2019 and 2020, respectively. There was an increase in the proportion of respiratory diseases among neonates, including congenital pneumonia and other respiratory conditions, and infections, including congenital sepsis, which reflects the direct and indirect effects of SARS-CoV-2 infection on pregnant women and neonates.