MLS Cup 2006 was the 11th edition of the MLS Cup, the championship match of Major League Soccer (MLS), and took place on November 12, 2006. It was contested between the New England Revolution and the Houston Dynamo to decide the champion of the 2006 season. The match was played at Pizza Hut Park in Frisco, Texas, which had hosted the previous cup.

Both teams qualified for the playoffs by placing second in their respective conference during the regular season. New England was appearing in their second consecutive final, while Houston had been formed from the relocated San Jose Earthquakes. The match was tied 1–1 on goals scored 71 seconds apart by Taylor Twellman and Brian Ching in extra time. Houston won 4–3 in the first penalty shootout in MLS Cup history, with Ching scoring the winning penalty kick and Pat Onstad saving the follow-up in the fifth round. Houston and New England would stage a rematch in the following cup, which the Dynamo won in Washington, D.C.