After graduating, Goucher continued to compete with a contract from Fila, running the fastest time for an American in 1999 in the mile (3:54.17), the sixth fastest for 3,000 meters (7:43.31), and third fastest for 5,000 meters (13:11.25). On consecutive days in February 2000 he won both the short (4K) and long course (12K) races at the USATF National Cross Country Championships under cold, muddy conditions in North Carolina. During 2000, he also made his first Olympic team, placing first in the Olympic Trials in the 5000 m. He was 13th in the 5000 m at the Sydney Olympic Games, despite serious battles with back troubles.