Bayerlein remained in the army and by the outbreak of the Second World War had reached the rank of major. In the invasion of Poland he served under General Heinz Guderian as his First General Staff Officer.
Bayerlein also served under Guderian during the Western Offensive. The crossed the Meuse near Sedan on May 14. However, General Paul von Kliest ordered Guderian to halt until the arrival of General Siegmund List and his 12th Army. This major mistake allowed the British Expeditionary Force to escape to England.
In October 1941, Bayerlein was sent to North Africa. When General Walther Nehring was wounded at Alam Halfa on August 30, 1942, he briefly became commander of the Deutsches Afrika Korps. He then served under General Erwin Rommel and General Wilhelm von Thoma. When Thoma was captured at El Alamein on November 4, Bayerlein once again resumed control during the retreat.
In October 1943, Bayerlein was sent to the Soviet Union as head of the 3rd Panzer Division. Three months later he became commander of the elite Panzer Lehr Division. They moved to Hungary before moving to France after the Normandy landings where he fought at Caen. Bayerlein also took part in the Ardennes Offensive under General Hasso Manteuffel. He got to within 10 miles of the Meuse before being forced to retreat.
Bayerlein was commander of the 53rd Corps until surrendering to the United States Army in the Ruhr on April 15, 1945. Fritz Bayerlein, who wrote a great deal about military matters after the war, died in 1970.