Upon completion of flight school, Pokryshkin joined the 55th GIAP (Gvardeyskiy Istrebitelnyy Aviatsionyy Polk, Guards Fighter Aviation Regiment) at Balti airbase near the Soviet-Romanian border at that time. Alexander devoted all his spare time in self-study of various disciplines which was likely to have had significant influence in the mastery of his profession. Another special period in Pokryshkins life was physical training: to control the machine in combat, a pilot needed great physical strength and a developed situational awareness. During his time in the 55th, Pokryshkin flew the I-15, I-153 and the MiG-3.

In the fierce battles during his war against experienced opponents, Pokryshkin soon realized the need to streamline the ways of conducting air combat. One of his self penned journals that came out of this was "Fighter Tactics in Combat", pilot notes” that were later passed to the Central Armed Forces Museum.

During the war, Pokryshkin was entrusted with the training of young pilots, teaching them everything he had learned by example. At the end the war, Colonel Pokryshkin was ordered to take command of the 9th Guards Air Division. He flew 650 combat sorties, in which he achieved 59 individual and 6 shared kills.