In 1941, at the age of 19, he was called up to fight in the Second World War with the Royal Navy, serving with the ranks of Ordinary Seaman, Able Seaman, and Leading Torpedo Operator. He was first assigned to PS "Bournemouth Queen", a converted excursion ship fitted for anti-aircraft guns, on duty off the coasts of England and Scotland. Beginning in 1943, he served on , a "Dido"-class light cruiser. There he saw action in 1943 in the Atlantic theatre, on two Arctic convoys and escorting aircraft carrier groups in operations against and other targets off the Norwegian coast. He took part in Convoy PQ 17 on "Royalist". In 1944 he and "Royalist" served in the Mediterranean theatre, as part of the invasion of southern France and in helping to sink blockade runners off Crete and bombard Milos in the Aegean. During this time MacLean may have been injured in a gunnery practice accident. In 1945, in the Far East theatre, MacLean and "Royalist" saw action escorting carrier groups in operations against Japanese targets in Burma, Malaya, and Sumatra. (MacLean's late-in-life claims that he was captured by the Japanese after blowing up bridges, and tortured by having his teeth pulled out, have been dismissed by both his son and his biographer as drunken ravings). After the Japanese surrender, "Royalist" helped evacuate liberated POWs from Changi Prison in Singapore.