In April 1941, the German Wehrmacht invaded Greece in order to assist the Italian assault. During this second wave of foreign invasion, the Luftwaffe eventually succeeded in destroying almost the entire Hellenic Air Force. However, some aircraft managed to escape to the Middle East, including 5 Avro Anson, 1 Dornier Do 22 and 3 Avro 626.
During the German occupation of Greece, the Air Force was rebuilt under the expatriated Greek Air Force Ministry based in Cairo. Three squadrons were built, operating under the command of the British RAF. These squadrons were the 13th Light Bombing Squadron flying Avro Ansons, Bristol Blenheims and Martin Baltimores and the 335 and 336 Fighting Squadrons flying Hawker Hurricane I and IIs and Spitfire V types. The RHAF squadrons in the Middle East flew a variety of missions, including convoy patrols, antisubmarine search, offensive patrols, reconnaissance, attack and interception of enemy aircraft. In Summer 1943, the Greek squadrons participated in the attack against the German Wehrmacht on the island of Crete and then from May to November 1944 in Italy. During those years, 70 Greek pilots were lost.
After Greece's liberation in 1944, RHAF returned to Greece and subsequently played a decisive role in the Greek Civil War, which lasted until 1950. By then, it was re-equipped with Supermarine Spitfire Mk IX, Spitfire Mk XVI fighters and Curtiss SB2C Helldiver bombers.