During World War II, Goodpaster commanded the 48th Combat Engineer Battalion in North Africa and Italy. He was awarded the Distinguished Service Cross, the Silver Star, and two Purple Hearts for his service in World War II. His combat experience was cut short in January 1944, when he was severely wounded and sent back to the United States to recover. After his wounds had healed, he was assigned to the War Planning Office under General Marshall, where he served the duration of the war.