After the beginning of Operation Barbarossa, Cheremisov remained with the 15th Army in the Soviet Far East. He was replaced in command of the army in November and became assistant commander for higher educational institutions of the Far Eastern Front. Cheremisov returned to army command on 8 September 1943 when he was appointed commander of the recently formed 16th Army. The army spent the rest of the war covering the Soviet–Japanese border on Sakhalin. He led the army in the Soviet–Japanese War as part of the 2nd Far Eastern Front, during which it conducted the Invasion of South Sakhalin and the Invasion of the Kuril Islands, being was promoted to lieutenant general on 8 September 1945.