On August 28, 1941, more than two months after Operation Barbarossa, the German invasion of the Soviet Union began, Pukhov was ordered to replace the commander of the 38th Army's 304th Rifle Division; this was his first field command since the rifle regiment about 15 years earlier. At the beginning of September it was transferred to the Kozelshchyna area, where until September 17 it suffered heavy losses in heavy defensive fighting, retreating east to the area of Sanzhery, Reshetylivka, and Poltava. The 304th then fought in the Donbass Defensive Operation during October, then was withdrawn to the reserve in the Snezhny Kut area. Pukhov held this position until January 20, 1942, when he was given command of the 13th Army, which he held until mid-1946. Until the middle of 1942 the army, part of the Bryansk Front, held defensive positions on the line of Skorodnoye and Kolpny. The army fought in the Battle of Voronezh in mid-1942 and the Voronezh-Kastornensk offensive operation in early 1943. On 14 February, following the latter, Pukhov was promoted to Lieutenant General. During the Battle of Kursk in July, the army, holding positions on the northern face of the Kursk bulge, repulsed six days of German attacks in fierce fighting, preventing a German breakthrough and limiting the German advance to 10–12 kilometers. When the Soviet troops switched over to the attack after decisively defeating the German army, the 13th Army fought in Operation Kutuzov.