In 2000, Thomas was traded to the MetroStars for Mike Duhaney, partially to help support Lothar Matthäus' adjustment to the United States.

As U.S. Soccer started to look abroad for players eligible to play for its national team in advance of its hosting the 1994 FIFA World Cup, Dooley was discovered.

Dooley became a regular for the U.S. almost immediately, being named U.S. Soccer Athlete of the Year in 1993 and then playing every minute at the 1994 World Cup, including the match against Colombia which the U.S. won 2–1.

Palami commended Dooley's ability to foster a better understanding of the game to his squad and give subs and reserves chances to step up in the absence of star players.

[12] Two months after the tournament, Stephan Schröck and Dennis Cagara resigned from the national team over tensions with Dooley.

[13] Schröck had disagreement with the setup of the national team under Dooley but has made amends with the coach in 2015 and briefly played once again for the Philippines though undisclosed issues surfaced in 2016.

[15] After an impressive run in qualifying that included a 3–2 win over North Korea that was considered an upset, Dooley's contract was extended for two years.

In January 2021, Dooley was appointed as head coach of Malaysia Super League club Sri Pahang, replacing Dollah Salleh.

[24][25] In May 2022, Dooley was reappointed as head coach of the Philippines national team ahead of the third round of 2023 AFC Asian Cup qualifiers, replacing Scott Cooper.