During the early months of the war, Cole-Hamilton was Commandant at the RAF's School of Army Co-operation.

With the evacuation of the British Expeditionary Force, Cole-Hamilton returned to Great Britain.

In December, Cole-Hamilton returned to an army co-operation training role, being appointed Air Officer Commanding (AOC) No.

October 1942 saw Cole-Hamilton appointed AOC of the Air Headquarters in West Africa.

Cole-Hamilton died aged 50 on 22 August 1945, less than four months after the end of the war in Europe, and was buried in St Giles' churchyard, Bradford-on-Tone, Somerset.