After the beginning of the German invasion of the Soviet Union, Operation Barbarossa, on 22 June 1941, Nikitin led the corps in the Battle of Białystok–Minsk as part of the Western Front. The corps fought in the area of Pukhovichy, on the Berezina River, and north of Bobruisk. After the corps lost all its tanks in an unsuccessful counterattack, it retreated to Mogilev, whose garrison Nikitin commanded during the Siege of Mogilev until being wounded and evacuated on 16 July. After the destruction of the corps, he was appointed deputy commander of the 49th Army. In this position, Nikitin participated in the Mozhaysk–Maloyaroslavets Defensive Operation, the Tula and Kaluga Offensives during the Battle of Moscow, and the Rzhev–Vyazma Offensive. He served as inspector of the cavalry of the Bryansk Front from March 1942. Red Army cavalry inspector General Oka Gorodovikov evaluated Nikitin's performance in this position as that of a "disciplined and demanding commander able to instill iron military discipline", before Nikitin went to Moscow on 1 August.