Macnee did not intend to pursue an officer's career, but nevertheless joined the officer's training corps at Eton. When his Second World War call-up papers arrived in 1942, he enlisted first as an Ordinary Seaman in the Royal Navy. According to his autobiography, Patrick was an Able Seaman when he returned to London after his six-week induction course.

Following a suggestion from his wife Barbara, whom Patrick had married in November 1942, he applied for officer status. Consequently, in early 1943 he was sent to HMS King Alfred, an officer's training establishment near Hove. There, he studied engine maintenance, flags, gunnery, navigation, Morse code, artillery, the use of torpedoes, and other such areas of naval expertise. After completing the course, he took additional training at Devonport and at the Royal Naval College at Greenwich, South East London.

After his commission as a navigator on Motor Torpedo Boats, he trained and served in the British Light Coastal Forces at Fort William in Scotland.
Having joined the First MTB Flotilla at Dartmouth, he participated in the naval battles of 1943 - 44 as a navigator aboard MTB 415. This vessel could sail at a speed of 38-40 knots, was equipped with machine guns, depth charges and torpedoes, and patrolled the English Channel from Cherbourg to Saint-Malo, protecting convoys and hunting for German submarines.

In 1944 Patrick was assigned as first lieutenant on the torpedo boat MTB 434, a ship that was to participate in the Allied invasion of Normandy, on "D-Day", 6th June. Although he arrived at Portsmouth to prepare for the invasion, when the day of sailing arrived, First Lieutenant Macnee was hospitalised with bronchitis in Chichester, and was therefore excused duty. During the fighting, MTB 434 was sunk by an enemy E-Boat off the coast of Normandy, leaving one crew member dead and several others injured. Patrick was informed of this news in hospital and to this day remains grateful for the fact that he was able to survive.

Ordinary Seaman	05.10.1942
Able Seaman	?
T/A/S.Lt.	06.1943
T/S.Lt.	04.12.1943
T/Lt.	04.12.1945