The former England stopper started working with the Cobblers in 2010 but quickly departed for Hull, only to soon return to Sixfields later in the year.
He duly took charge of one match as caretaker manager in November 2011 before being replaced by Aidy Boothroyd and returning to his role as goalkeeping coach.
Following Boothroyd's recent sacking in December, Flowers assisted Town's caretaker boss Andy King until the appointment of new manager Chris Wilder this week, a move which has also seen King part ways with the club.
Wilder told Town's official website: "I would like to thank Tim for his work on behalf of the club.
"I know Tim has been a long-serving goalkeeping coach here and he has served the club with distinction for a number of years.
"I am sure all Cobblers fans will join me in wishing Tim every success for the future."
Meanwhile, Gillingham striker Antonio German has extended his loan stay at Northampton by a further month while Hallam Hope has returned to parent club Everton.
- Sports & Recreation
- Aidy Boothroyd