Goucher's career has been plagued with injury. Despite having continually been ranked as one of the foremost American competitors at distances between 1500 m and 5000 m, he was prevented from performing optimally at the 2004 Olympic Trials by an Achilles heel problem and thus did not qualify for the Olympic team. The Olympic Trials were a culmination of a very rough period for him and soon thereafter he left Mark Wetmore, his longtime coach and friend, to train with Alberto Salazar in Oregon.
The move proved beneficial for Goucher. Goucher's 2005 season saw him improve his 5000 m time to 13:10.19 and take 2nd place at the USA Cross Country 4 km Championships.
In 2006, Goucher ran a 10:50 at the USA Cross Country Championships to win first place in the short course (4 km). He went on to finish 6th in the short course race at the IAAF World Cross Country Championships in Fukuoka, Japan, the highest finish by an American since Pat Porter placed 6th in the 1986 World Cross (12K) Championships. He finished only 8 seconds behind the winner, world-renowned Ethiopian champion Kenenisa Bekele, the 5k and 10k world record holder. At the 2006 Prefontaine Classic, Goucher finished third in the 2 mile with a time of 8:12.7, the third fastest 2 mile ever run by an American.
Goucher's performance at the World Cross Country meet and his 2 mile at the Prefontaine Classic were the highlights of a year that also saw him dipping under 28 minutes for the 10,000 meters with a 27:59.41 at the Van Damme Memorial Meet in Brussels, Belgium.