The team was created on December 15, 2005 when the San Jose Earthquakes were relocated, due to owner AEG's failure to secure a soccer-specific stadium. Even though all of San Jose's players and coaches moved to Houston, the team's name, logo, history and statistics were not transferred and remained inactive in San Jose thus making the Dynamo a new team, similar to the Baltimore Ravens in the NFL.

The Dynamo played their first game on April 2, 2006. Amidst a crowd of 25,462 people in Robertson Stadium, the Dynamo beat the Colorado Rapids 5–2. Brian Ching led the charge for the Dynamo with four goals, all of which were set up with assists from teammate Dwayne De Rosario. In stoppage time, Alejandro Moreno scored MLS' Goal of the Week with a game-clinching bicycle kick. On May 6, 2006, the Houston Dynamo won their first intrastate rivalry game against FC Dallas, 4–3 at Robertson Stadium.

The Dynamo finished their first season in Houston with an 11-8-13 record, good for second place in the Western Conference. They lost the first game of the two-legged conference semifinal to C.D. Chivas USA, 2-1, on October 22 in Los Angeles. Chivas goalkeeper Brad Guzan stopped De Rosario on a penalty kick that could have tied the match.

In the second leg on October 29, Houston defeated Chivas USA 2-0 at Robertson Stadium, advancing in dramatic fashion. After a red card to Chivas' Juan Francisco Palencia, Houston's Brad Davis converted a second-half penalty kick to tie the aggregate score. With the match in second-half stoppage time, Brian Ching headed in the winning goal from close range to delight the crowd of more than 17,000.

On November 5, 2006, the Dynamo defeated the Colorado Rapids 3-1 in the Western Conference final to earn a spot in its first MLS Cup. Scottish forward Paul Dalglish scored twice in front of an MLS Cup Playoffs-high crowd of 23,107.

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