In 1939, he commanded the 10th Army during the Polish campaign. As of 1941, he was deputy commander of the Central and Byelorussian fronts and he commanded the 49th Army of the Soviet Union, playing a key role early on during the Battle of Moscow in late 1941. There, he was placed by Zhukov in Kaluga as part of the Mozhaisk Defence Line, which contributed greatly in slowing down the German advance toward Moscow. They were able to stop the XIII Army Corps near Serphukov and by mid-December, they were able to launch a counteroffensive. During the Soviet counterattack in early 1942, he led his troops in Tula, Kaluga, and Rzhev. During the Rzhev-Vyazma operation, the 49th Army liberated the city of Yukhnov and by 20 April had reached the Ugra river. In March 1943, the army under the command of Zakharkin participated in the Rzhev-Vyazma offensive (1943), advancing in the direction of the Spas-Demensk. On 18 September 1943 Zakharkin was promoted to colonel general. On 23 March he was appointed commander of the Odessa Military District. He died in a car crash on 15 October 1944 and was buried in Odessa.