The pandemic caused by the SARS-CoV-2 virus has put a huge strain on health systems around the world. Clinical trials of new drugs were also influenced by the pandemic, during which Sponsors came across a number of problems, including ensuring patient safety and maintaining the ability to obtain reliable data in the course of ongoing research. The purpose of this study was to compare the protocols of clinical trials of two Sponsors, approved by the Russian health authorities for three years, from 2017 to 2019, by their adaptability to the SARS-CoV-2 virus pandemic. 23 protocols and 51 amendments were studied in total. The amendments published in 2020 by both Sponsors underwent a comparative analysis to determine the degree of their influence by the pandemic. Statistical processing of the results was carried out using the correlation analysis. Conclusions were drawn about the Sponsors’ approach to clinical trial planning and establishing the safety margin of clinical trial protocols.