On January 18, 2010, Brown was hired as an assistant head coach for Real Salt Lake. He would assume the vacancy left by Robin Fraser, who left the club to coach Chivas USA. On December 11, 2013, Brown was named assistant coach of the Chicago Fire, where he won an MLS Cup as a player in 1998. After almost a year he moved to expansion club New York City FC on December 1, 2014, rejoining Jason Kreis, who he had worked under at Real Salt Lake.