The 42-year-old, who played 169 league games during four years with the Cobblers, becomes technical development manager and under-16s coach.
Last season he was assistant to Jon Brady at Brackley Town.
Northampton appointed Sean Parrish as their new head of youth and Trevor Gould as head of the centre of excellence in June.
Rotherham-born Warburton started out at his hometown club before spells at York, Rushden, Boston and finally Aldershot.
The changes have coincided with boss Ian Sampson's decision to focus the club's efforts on producing talented youngsters.
Source: BBC Sport
Source: BBC Sport