Following the outbreak of the Second World War, Honner enlisted in the Second Australian Imperial Force (2nd AIF) on 24 October 1939. In December 1939 he took command of 'C' Company of the &lt;a href="2/11th%20Battalion%20%28Australia%29"&gt;2/11th Battalion&lt;/a&gt;, a Western Australian infantry battalion, with the rank of captain. Honner and his battalion sailed for the Middle East in April 1940, arriving the following month. After undertaking training in Palestine, Honner's company then proceeded to fight in the battles of the Western Desert campaign against the Italians at Bardia, Tobruk and Derna before being dispatched to Greece following the German invasion in April 1941. In Greece, Honner led his men through a series of fighting withdrawals as they were pushed back by stronger German forces. Later they were evacuated to Crete where they took part in the heavy fighting around Retimo. Honner then led a group across the island in order to evade capture and, after meeting up with a Royal Navy submarine, they were evacuated to Alexandria. He was subsequently promoted to major and, for his leadership during the fighting around Thermopylae in the earlier Greek campaign, he was awarded the Military Cross.