Yegipko commanded submarine brigades after his return to the Soviet Union, including during the Soviet-Finnish War, and after the German invasion of the Soviet Union in June 1941, participated in the Soviet evacuation of Tallinn in August 1941. During this time his submarine, "S-5", was sunk by a mine, and Yegipko had to be rescued from the water after being blown overboard. He then became naval attaché to the United Kingdom and was an observer on several of the Arctic convoys, including the disastrous Convoy PQ 17. The later war years were spent with the General Staff of the Armed Forces, after which he held several posts in naval education and academia, ending as head of the . He retired in 1967 and wrote his memoirs before his death in 1985.