At the start of the war, she was reassigned to the Third Destroyer Division of the Baltic Fleet. During the evacuation of the Soviet Navy from Tallinn to Kronstadt during Operation Barbarossa, "Yakov Sverdlov" was assigned as an escort to the flagship . During the operation, she hit a mine and sank near Cape Juminda on 28 August 1941. The wreck was located and identified on 16 June 2018; lying at a depth of , the ship is broken into two pieces.