The 64-year-old has had spells in charge of a number of clubs, including Manchester City, Brighton & Hove Albion and Macclesfield Town, during his 29-year coaching career.
Horton will now help manager Paul Dickov as the team prepare for life in the Championship after gaining promotion from League One.
"It's brilliant to be here," he told the club's official website. "It's a great club with a fantastic training ground and stadium, and with promotion to the Championship last season I'm really looking forward to it."
Doncaster start the season at Blackpool on August 3.