He was drafted by the then San Jose Clash in the third round of the 1996 MLS College Draft. He would spend the next four years in San Jose, becoming a full-time starter in his second season. Originally a forward, the lefty moved to the midfield early on in his pro career. In his time with the Clash, he scored nine goals and added 35 assists in 115 games and was named to the MLS Best XI in 1999.

Lewis signed with England's Fulham, then in the Football League First Division, in 2000. He spent three seasons there, but did not see much playing time, especially in his last year, when the club was promoted to the Premiership. He only played one game for his club in 2001-02, the meaningless season finale. Overall, he appeared in 14 total games for the London club, scoring just one goal. Lewis made a move to Preston North End in 2002 and spent the next three years there, a consistent starter throughout his tenure. He transferred to Leeds in June 2005.

Lewis made his debut with the U.S. national team on October 16, 1996, against Peru, a game boycotted by almost all regular US players because of salary concerns. Unlike most of the other players to appear in that game, Lewis went on to have a long national career, compiling 67 caps as of December 2005. He played an important role for the US in the 2002 World Cup, starting both elimination games, and delivering a cross to Landon Donovan for the team's second goal in their 2-0 victory over Mexico. With increasing competition at left midfield, most notably from DaMarcus Beasley, Lewis began a transition to left back in late 2005, debuting in that slot in a World Cup qualifier against Trinidad & Tobago on August 17, 2005. Although he continues to play left midfield for his professional club, Lewis has welcomed the move to left back for the national team and appears to be on the way to securing a permanent role in that position. On May 2nd, 2006, for the second successive time, Lewis was named to the US roster for the FIFA World Cup in Germany.