By July 1940, during World War II (although the United States was still neutral at this point), he was a G-3 staff officer with I Armored Corps. He served with the corps until July 1942, seven months after the American entry into the war, which occurred due to the Japaneseattack on Pearl Harbor on December 7, 1941.
In April 1943, when the campaign in North Africa was coming to an end, he was promoted to the two-star general officer rank of major general and a month later became commanding general (CG) of the 2nd Armored Division, replacing Major General Ernest N. Harmon. At the age of 47, Gaffey was one of the youngest division commanders in the U.S. Army at the time. He commanded the division in the Allied invasion of Sicily (codenamed Operation Husky) in the summer of 1943 where, fighting in difficult mountainous terrain and operating in very hot weather, the division, advancing some 200 miles and facing light resistance, captured the Sicilian capital of Palermo along with thousands of Italian soldiers. The 2nd Armored Division, under Major General Gaffey, was sent to England later in the year to train and spearhead the Alliedinvasion of Normandy (codenamed Operation Overlord), scheduled for the following year.
In June 1946, Gaffey was the CG of Fort Knox, Kentucky when he was killed in a B-25 Mitchell crash as it attempted to land at Godman Field, Kentucky. He was buried at the post cemetery.