Shortly after Operation Barbarossa, the German invasion of the Soviet Union, began, the 1st Motor Rifle Division was rushed to the Western Front in late June 1941. Baklanov was soon promoted to command the 175th Motor Rifle Regiment of the division, but he was wounded near Orsha during the border battles. Upon recovery in November he was made commander of a battalion of students at the Omsk Infantry School. Returning to the front in January 1942, Baklanov took command of the 157th Rifle Brigade, part of the 11th Army of the Northwestern Front, distinguishing himself in fighting at Staraya Russa. Transferred south to command the 299th Rifle Division in June 1942, he led it in the Battle of Stalingrad as part of the 66th Army. 66th Army commander Rodion Malinovsky evaluated Baklanov as a "personally brave, strong-willed, and demanding commander...quickly acquiring experience in division command...a developing, capable commander." He was awarded the Order of Alexander Nevsky and the American Distinguished Service Cross for his actions at Stalingrad, and promoted to major general on 1 March 1943.