Clark began 2007 by making his continental debut in the 2007 CONCACAF Champions' Cup, appearing in three of Houston's four games against Puntarenas and Pachuca. He then missed more than a month of the 2007 season on national team duty, appearing in the 2007 CONCACAF Gold Cup and 2007 Copa América. His play through the first half of the season, including a goal against FC Dallas on June 3, earned him a spot in the 2007 MLS All-Star Game, the second consecutive season that Clark had been selected as an all-star. Following his return from the United States squad, he scored for the second time on the season on September 16, in a 3–1 victory over LA Galaxy. However, Clark's season ended at the end of September. He missed the final two regular season and all playoff matches due to a suspension resulting from a deliberate kick aimed at a prone Carlos Ruiz in a match with FC Dallas on September 30. Clark was sent off, received a nine-game suspension, and was fined $10,000, the most severe punishment in MLS history. In his absence, Houston went on to win MLS Cup 2007, repeating as MLS Cup champions. Clark finished the season with 23 appearances and two goals across all competitions.