In 1940 Troughton enlisted with the Royal Navy, receiving a commission as a lieutenant with the RNVR. He was deployed on East Coast Convoy duty from February to August 1941, and then with Coastal Forces' Motor Gun Boats based at Great Yarmouth from November 1942 to 1945, operating in the North Sea and English Channel. During his service with the MGBs he was on one occasion involved in an action against Kriegsmarine E-boats which resulted in one of the enemy craft being destroyed by ramming, whilst Troughton's boat and another destroyed two more with their gunfire. His decorations included the 1939–45 Star, and Atlantic Star, and he was Mentioned in Dispatches "for outstanding courage, leadership and skill in many daring attacks on enemy shipping in hostile waters". He used to wear a tea cosy on his head in cold weather in the North Sea.