He joined No 5 Commando in July 1940 at its inception from the Royal Signals. The War Office was concerned by the lack of mountain troops and asked that Soldiers with a knowledge of climbing come forward. He had been taught climbing by the Chemistry Master at Eastbourne College where he was teaching maths and physics. He volunteered and was stationed at the Clachaig Hotel in Glencoe where he and his comrades ran a course for several months and proved to the War Office that ordinary troops could be turned into mountaineers. In May 1942. he accompanied 5 Commando, part of the 29 Infantry Brigade, in the invasion of Madagascar against the Vichy French. His objective was a large battery which covered the beach since its capture would enable the main force to take the port of Diego Suarez frrom the rear. Rees-Jones led the first 2 landing craft and, at 2.00am, was the first of his unit ashore. He said afterwards:- "We caught the French fast asleep. There was a proper scrap, but we took the battery without a casualty."

In 1943 the Commando Mountain and Snow Warfare Training Centre moved to North Wales under the command of Rees-Jones and the Lovatt Scouts were trained there as a mountaineering battalion. The War Office decided that the commandos needed more shore work and that the training centre should become a Cliff Assault School The centre was moved to St. Ives in Cornwall to train in cliff assaults in preparation for the D-Day landings. Rees-Jones pioneered the concept of using small boats called "dories" to land commandos on otherwise inaccessible beaches.

The night before D-Day he escorted a raiding party up a Normandy cliff to capture a shore battery. After attending Staff College, he was posted to Germany as Brigade Major of 4 Cmmando Brigade and was mentioned in despatches.