The 63-year-old, the club’s manager from 1989-2001, has ended any speculation about his future.
Bryan Hughes’ number two will carry on at the Racecourse as the club look to put in another promotion challenge.
Flynn said: "Obviously my key aim is to get Wrexham back to where they belong and to assist Bryan in that huge task.
"If I can help in any way, whichever form that is, I am more than willing to do that.
"I'm back in with Bryan and the staff as well because he has got some good staff, and I will help as much as I can."