April 1, 2006 and scored his first MLS career goal helping FC Dallas to a 3–2 victory against the Chicago Fire. Cooper made his first MLS start the following week against Real Salt Lake on April 8, 2006 scoring the team's first goal in a 2–1 victory. He finished his first MLS season tied for sixth in goals scored with 11 and made 31 appearances. At the start of the 2007 MLS Season, Cooper scored four goals in the first eight games before he suffered a broken right tibia in a 3–1 win against the Los Angeles Galaxy by a strong tackle from Tyrone Marshall that put him out for a majority of the season. This ended his hopes of playing in the 2007 Copa América and for the national team. Cooper ended the 2007 season with a total of 12 starts out of 14 appearances, four goals, and two assists.