In 1996, he was selected by MetroStars in second round of the Inaugural MLS Draft. Troy, who had strong roots in the San Francisco Bay Area, refused to sign with the league and move his family to the New York area. Therefore, he was traded by the MetroStars to the San Jose Clash in exchange for Rhett Harty and first round pick in 1996 College Draft. He was a solid starter for the Clash until, in August 1997, he suffered a violent collision snapping his head backwards. Troy's neck was already aggravated due to two previous neck injuries, and he was very close to becoming paralyzed. Troy was told that he would never play again. Nonetheless, in October 1997, he underwent surgery that fused a piece of bone from Troy's hip onto his 5th and 6th vertebrae. After a long march to recovery, he rejoined the Clash in 1998, going on loan to the San Francisco Bay Seals for one game, only to be waived at the end of the season. In 1999 Dayak signed with the San Francisco Bay Seals of the A-League. Early in the 1999 season, Dayak suffered a major knee injury damaging his medial collateral ligament and posterior cruciate ligament. After a difficult recovery complicated by infection, Troy rejoined the Seals for the 2000 campaign as a player and coach. He was honored that season when he made the A League all stars. In 2001 Troy was signed by Frank Yallop, new head coach of the San Jose Earthquakes. When not suffering from a multitude of injuries, Troy has been a solid starter for the Quakes, helping lead the team to two MLS Cups in 2001 and 2003. Dayak earned the MLS Comeback Player of the Year Award in 2001. Dayak has scored eight goals and added seven assists in his seven years in the league.
Troy has announced that he would retire after the 2005 MLS season. Even before his retirement became official, he was named head coach for the MISL expansion franchise, the California Cougars, who are based in Stockton, California.
Post-retirement
June 2, 2005, Dayak was the Technical Director of the Livermore Youth Soccer League in Livermore, California. He is now the Founder and Director of Coaching for West Coast Soccer Club which is rapidly becoming one of the most dominant youth soccer clubs in the country. He holds a National "A" coaching license and in 2007 earned his NSCAA Director of Coaching Certification. Troy owns a retail soccer store in Tracy, California, as well as an alfalfa farm. Married to wife Karen, they have two children, daughter Adaurie and son T.J. He also provided color analysis for CSN Bay Area and CSN California broadcasts of San Jose Earthquakes games for the 2008 and 2009 Major League Soccer seasons.