Barker has worked alongside Karl Robinson at League One Charlton since December 2016 but was approached by Rotherham last week.
The 41-year-old had three spells with the Millers as a player, scoring 13 goals in 153 league games.
Rotherham will join Charlton in League One next season following their relegation from the Championship.
Barker and Warne were team-mates when the Millers won promotion to the second tier 2000-01.
Rotherham United have appointed their former player Richie Barker as assistant to manager Paul Warne.