Horton began his coaching career the same place he began his collegiate playing career, Cerritos College. He coached there for two seasons before moving onto Los Angeles Valley College. From there he went back to Cerritos College as an assistant before eventually becoming the head coach. He was later hired by his former coach, Augie Garrido, to be an assistant at Cal State Fullerton. When Garrido left in 1996, Horton was hired to replace him.[4]
In 2003, Horton was named 2003 National Coach of the Year by Baseball America.[5]
In 2004, Horton would face off against his old boss in the 2004 College World Series championship series. The Fullerton Titans won the series and the national championship.
In September 2007, Horton was named the head coach of the University of Oregon, which reinstated its baseball program starting in the 2009 season after being a club sport since 1982.[6] In his first season at the helm of the Ducks the team was 14–42.
In 2010, Horton led the Ducks to the NCAA Division I baseball Tournament for the first time since 1964. The 2010 Ducks baseball team finished the season with a 40–24 overall record. On May 28, 2019, Horton and Oregon mutually agreed to part ways.[7]
National champion
Postseason invitational champion
Conference regular season champion
Conference regular season and conference tournament champion
Division regular season champion
Division regular season and conference tournament champion
Conference tournament champion