In contrast to many other officers who took part in that war, he was not purged after his return to the Soviet Union,[2] and was made the Head of the Directorate of Tank and Armoured Car Troops of the Red Army which gave him considerable influence on its development.

In the fall of 1940, Georgy Zhukov started preparing the plans for the military exercise concerning the defence of the Western border of the Soviet Union, which at this time was pushed further to the west due to the annexation of eastern Poland.

[citation needed] Pavlov chose to watch the comedy to its end and this proved to be a fatal mistake in the eyes of his superiors in Moscow.

During the first days of the invasion, Pavlov was relieved of his command, replaced by Andrey Eremenko (and again by Semyon Timoshenko), arrested and accused of criminal incompetence and treason.

He and his chief of staff Vladimir Klimovskikh were first accused of: As the members of the anti-Soviet military conspiracy, betrayed the interests of the Motherland, violated the oath of office and damaged the combat power of the Red Army that are crimes under Articles 58-1b, 58-11 RSFSR Criminal Code ... A preliminary judicial investigation and determined that the defendants Pavlov and Klimovskikh being: the first – the commander of the Western Front, and the second – the chief of staff of the same front, during the outbreak of hostilities with the German forces against the Union of Soviet Socialist Republics, showed cowardice, failure of power, mismanagement, allowed the collapse of command and control, surrender of weapons to the enemy without fighting, willful abandonment of military positions by the Red Army, the most disorganized defense of the country and enabled the enemy to break through the front of the Red Army.Pavlov and his deputies were accused of "failure to perform their duties" rather than treason.

On 22 July 1941, the same day the sentence was handed down, Pavlov's property was confiscated, and he was deprived of military rank, shot, and buried in a landfill near Moscow by the NKVD.