Traded To New England
In the summer of 1999, Harkes returned to the States to play for the New England Revolution, who had acquired his rights in a trade with United. While Harkes was again captain of the team, it was also a struggling franchise. However, the team had its best season ever with a 13-13-6 record. Also in 1999, he was asked to be on the U.S. national team again by its new coach, Arena. Harkes played for them in the Confederations Cup.
Harkes was again traded within the MLS in May 2001 to the Columbus Crew. Though he had issues with how the trade was handled, his new team made the playoffs. After re-signing with the Crew in the off-season, the team won the Lamar Hunt U.S. Open Cup in 2002.