Kupriyanov was elected as the First Secretary of the Karelian Regional Committee of the Communist Party in June 1938 on the recommendation of Andrei Zhdanov to Stalin. As a regional committee's First Secretary, Kupriyanov became part of the NKVD troika in September 1938. During the Winter War, he ordered the construction of the 132 kilometer-long Petrozavodsk-Shuezersk railway; the railway was built in 46 days. With the formation of the Karelo-Finnish SSR in 1940, he became the First Secretary of the Communist Party of the Karelo-Finnish Soviet Socialist Republic on April 2, 1940. He was elected as a candidate member of the Central Committee of the All-Union Communist Party (Bolsheviks) during the 18th Party Congress. Gennady Kupriyanov and his family were evacuated to Novosibirsk in August 1941 due to World War II. He was removed from his post on January 25, 1950, due to the Leningrad Affair.