Arapov graduated from the academy in October 1941, after the German invasion of the Soviet Union, and became assistant chief of the 1st Separate Staff Operations Department of the 50th Army, part of the Bryansk Front and from November part of the Western Front. He participated in the Battle of Moscow and the defense of Tula and Plavsk. In the defenses of the two cities, Arapov was reported by his superiors to have "skillfully coordinated the operations of the combat units." During the battle for Tula, as the representative of the army staff, Arapov "skillfully combined his personal courage with the ability to manage the troops, ensuing the fulfillment of orders." During the Vyazma airborne operation in January and February 1942, Arapov made dozens of flights to troops of the 4th Airborne Corps, dropped in the rear of German Army Group Centre, to coordinate their operations with those of the 50th Army. For his actions, Arapov was promoted to major on 22 January and awarded the Order of the Red Banner on 31 January.