Flowers, 43, had a short spell working with the keepers at Sixfields last season before leaving to become Iain Dowie's assistant at Hull City.
But now he is back at Town in place of Paul Crichton, who has accepted a post with a Championship club.
"The move has worked out well for all parties," commented Cobblers manager Ian Sampson.
"Paul has got a good opportunity for him and, after leaving Hull, Tim was available.
"We are only too pleased to have him back. He has a wealth of experience, the keepers here liked working with him last season. "
"I think it's a sign of the calibre of work we do with our young goalkeepers that both Tim and Paul have been wanted by higher division clubs," Sampson added.
"Tim is back working with us that's good news for the club - and particularly for Chris Dunn and Paul Walker who'll be delighted to team up with him again."
Flowers was a regular for Southampton, Blackburn and Leicester in his playing days, and won 11 England caps in the 1990s.
Source: BBC Sport
Source: BBC Sport