In January 1960, he commanded the heavy cruiser . In July 1960, Kauffman was selected as Rear Admiral, and he became Commander Destroyer Flotilla Three (later redesignated Cruiser Destroyer Flotilla Three). In 1962, he became Chief of the Strategic Plans and Policy Division. In 1965, he became the 44th Superintendent of the U.S. Naval Academy, where he served for three years. His next assignment was as the Commander of the U.S. Naval Forces in the Philippines, and Representative of the Commander-in-Chief, Pacific, a billet once filled 25 years earlier by his father. In June 1970, he became commandant of the 9th Naval District, headquartered at Great Lakes Naval Station, Illinois, with an additional duty as Commander of the Station. Rear Admiral Kauffman retired from the Navy on 1 June 1973 and became the 9th president of Marion Military Institute from 1974 to 1976. He died in 1979. The , launched in 1987, was named in honor of Draper Kauffman and his father, Vice Admiral James L. Kauffman (1887–1963). His roles as the founder of U.S. Naval Bomb Disposal and as the founder of the UDT/SEALs were also commemorated in the creation of the Kauffman EOD Training Complex at Eglin AFB, Florida, and the Draper L. Kauffman Naval Special Warfare Operations Facility in Norfolk, Virginia. His great-niece named her first-born child after her great uncle. Professor Kelsey Kauffman, of DePauw University, is his daughter and is an author. Taren Stinebrickner-Kauffman, founder of SumOfUs, is a granddaughter.