Also an All-American midfielder for the Greyhounds' lacrosse team, Thornton transferred to Loyola after playing two years at Essex Community College, where he compiled a 26-4-1 overall record and earned first-team All-NJCAA honors.
Thornton made his MLS debut with MetroStars in 1996, playing two seasons, before the Chicago Fire picked him up in the 1997 MLS Expansion Draft. Thornton led the Chicago Fire to the MLS Cup and U.S. Open Cup titles in 1998 - the club's inaugural season, and he earned MLS Goalkeeper of the Year and MLS Best XI honors that year, in addition to making his first MLS All-Star team.
In nine seasons with the Fire, halted only by a six-month contract with Portuguese club Benfica in 2004, Thornton helped the club win four U.S. Open Cup Championships and its first-ever MLS Supporters Shield title as regular season champions (2003). The second goalkeeper in MLS history to reach 100 wins, he was also a five-time MLS All-Star with the Fire and was named the Chicago Fire Defender of the Year in both 2001 and 2002, in addition to being honored as the club's MVP in 2002.
Thornton spent the next two years with the Colorado Rapids (2007) and New York Red Bulls (2008) before a trade brought him to Chivas USA midway through the 2008 season. He started both of the club's playoff games that season before leading the league in both goals-against average (0.87) and shutouts (12) in 2008. He was named to his sixth MLS All-Star team that year and later earned the titles of MLS Goalkeeper of the Year, Comeback Player of the Year, Best XI and Chivas USA MVP.
Internationally, Thornton became a member of the U.S. National Team in 1994 and he backed up Kasey Keller at the 1996 Summer Olympics.