Don Clary was born in Anchorage, Alaska, and graduated from East Anchorage High School in 1975. Clary had his first success as a junior (under-20) athlete at the 1975 IAAF World Cross Country Championships where his fifth-place finish took the American juniors to the team title, alongside Bobby Thomas, Roy Kissin, and Ralph Serna. He went on to attend the University of Oregon and ran for the Oregon Ducks collegiate team. At the 1978 NCAA Division I Men's Cross Country Championships he placed seventh and was runner-up in the team rankings alongside classmate Alberto Salazar. He ran the 3000-meter steeplechase at the 1978 USA Outdoor Track and Field Championships and reached seventh place. He won his first national title that year, however, doing so in the one hour run.