After the first Pe-2 aircraft of the first series entered service with the Soviet Air Force in spring 1941, pilots immediately noticed the inadequacy of the course and defensive armaments. To remedy these shortcomings, starting with the thirteenth series, one of the ShKAS course machine guns was replaced with a large-caliber UB machine gun, and the same was done for the under-fuselage defensive position. The first major redesign based on pilot feedback was the Pe-2 31 series, which began production in the summer of 1941. Two of the five windows on the right side of the nose were replaced with a single triangular window, improving access to the nose machine guns for mechanics. Several other minor changes were also made. Aircraft of this series were produced until spring 1942.

The Pe-2-31 was introduced before the beginning of Open Beta testing. It is a fast, maneuverable dive bomber with an extremely high structural limit speed. However, its armor and defensive armament are weak, and the aircraft is quite large. Only the pilot and one of the two gunners are protected by armor. The Pe-2-31 differs from the original Pe-2 series in that it has reinforced main and defensive armaments, armor for one of the gunners, and the ability to mount unguided rockets. There are also minor visual changes.