At the age of 42, in 1918 he became Minister of War and Commander of the Ottoman Army. In 1920, he followed Mustafa Kemal to Samsun, and supported him throughout the Turkish War of Independence. His support provided Mustafa Kemal with the full support of the Armed Forces, which was reduced to two armies in the aftermath of the disarmement dictated by the Treaty of Sèvres. These two armies were under the command of Kazım Karabekir on the Eastern Front based in Erzurum and Ali Fuat Cebesoy on the Western Front based in Ankara. Fevzi Çakmak was one of the few significant generals of the Turkish War of Independence.
With Mustafa Kemal in Izmir, 1922, after the victory in the War of Independence.