In 1936, al-Qawuqji began fighting the British and the Jewish population in the Mandate of Palestine in actions that would become known as the 1936–39 Arab revolt in Palestine. He represented the Iraqi 'Society for the Defense of Palestine' which was separate from forces under the control of Grand Mufti of Jerusalem Haj Amin Husseini. Al-Qawuqji resigned his commission in the Iraqi army and his position at the Royal Military College to lead approximately fifty armed guerrillas into Palestine. In June he contacted Fritz Grobba, who was acting as German ambassador to Iraq. This was probably al-Qawuqji's first encounter with a representative of Nazi Germany. In August, he commanded about 200 volunteers from Iraq, Syria, Transjordan, and the Samaria region of Palestine. His title was 'Supreme Commander of the Arab Revolution in South-Syrian Palestine.' He operated four units, (Iraqi, Syrian, Druse, and Palestinian) in the Nablus - Tulkaram - Jenin triangle until the end of October. The military performance of al-Qawuqji's troops became hampered by internal dissensions and animosity between him and Grand Mufti Husseini, the Arab Higher Committee, and the Mufti's kinsman Abd al-Qadir al-Husayni, who commanded forces that were active in the area around Jerusalem. On October 26, 1936, al-Qawuqji crossed the Jordan River with his troops into Transjordan. A few weeks later he returned to Iraq.

Collins and LaPierre summarization of al-Qawuqji's pre-WWII career includes the observation that "The high point of his military career had come during the Arab revolt against the British in Palestine in 1936."

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