The former Middlesbrough defender had worked in a similar role under new Bolton manager Dougie Freedman and assistant boss Lennie Lawrence at Crystal Palace.
Fleming, who earned 10 caps for the Republic of Ireland between 1996-98, retired as a player in 2005 and became youth-team coach at The Riverside before joining Scottish side Livingston as assistant manager.
The 44-year-old, who also played for Birmingham, Palace and Darlington, joined the coaching set up at Selhurst Park in July 2011.
- Sports & Recreation
- Dougie Freedman
- assistant manager
- Lennie Lawrence