Warner attended Denver East High School, played club soccer for Colorado Rush, and spent time training with English Premier League players and coaches at the Liverpool Youth Academy in 2002, before playing four years of college soccer at the University of Portland. He was named to the All-West Coast Conference Freshman Team and received an All-WCC Honorable Mention as a rookie in 2006, was named to the All-WCC First Team and to Top Drawer Soccer’s All-Season Third Team in 2007, and was named to the All-WCC First Team for the second consecutive year in 2008, when he led the Pilots with eight assists and was second on the team with five goals.

Warner was drafted in the first round (15th overall) of the 2010 MLS SuperDraft by Real Salt Lake. He made his professional debut on April 17, 2010, in a game against Los Angeles Galaxy. Warner went on a short-term loan to USSF Division 2 club AC St Louis on July 28, 2010.

Warner was left exposed by Real Salt Lake in the 2011 MLS Expansion Draft and was selected by expansion side Montreal Impact.

Warner was traded to Toronto FC for Issey Nakajima-Farran on May 16, 2014.

Warner was traded to Houston Dynamo for a second round draft pick on March 2, 2016.

On December 13, 2016 Minnesota United FC drafted Warner in the second round of the 2016 MLS Expansion draft.

On 17 April 2019, FC Helsingør announced the signing of Warner on a free transfer. The deal ran out to the end of the season.

On June 30, 2020, Warner signed a one-year deal with Colorado Rapids.