Hogan came into his own starting in 1940. He had a three-tournament winning streak in March of that year, and although he only won one more that year he was still the tour's leading money winner for 1940. He was on top again in 1941, with five tournament wins, and again in 1942. Also, in the spring of 1941, Hogan returned to Hershey as its club professional. At that club, Hogan had no responsibilities to give lessons or otherwise interact with the fellow members: all he had to do was play in tournaments, provide publicity for the club, and play the course often enough that the members could observe him and attempt to learn from what they saw. For this, he received several thousand dollars per year.
The one thing lacking for Hogan was a win in a major tournament, and the entry of the United States into World War II and the accompanying decrease in the touring schedule deprived him of several chances from 1942 on. Hogan did win the Hale America Open in 1942, which was held in lieu of the U.S. Open, but this was not technically a major. At the Masters, the only official major to be held that year, Hogan tied with Nelson in the first three rounds, only to lose by one during a playoff round the next day.
The tour was officially suspended in 1943, and in March of that year Hogan was drafted. He trained to become a flight instructor, went to Officer Candidate School, and eventually became a captain. He continued to play golf as often as he could, including a weekly round with the commander of his base for a time, and in 1944 when professional golf resumed Hogan made it to a few tournaments. He was discharged in August of 1945 and rejoined the tour almost immediately.
Nelson had not been drafted because of a medical condition, so he had spent the war years working on his golf full-time, playing war-benefit exhibitions in 1943 when there was no tour. With so many other players off to war, Nelson had been the undisputed champion in 1944 and early 1945. Although Hogan had not been practicing with his usual ferocity for more than two years, he quickly challenged Nelson for the top spot. Although the major championships again eluded him, he won thirteen of the thirty-two tournaments he entered, becoming the Professional Golfers' Association of America champion and the top money-winner of 1946.