Gilligan, 24, is one of just seven players under contract for next season but the club's longest serving player has been told his future lies elsewhere.
The former Watford academy product has made over 200 appearances for the Cobblers and spent a spell on loan with Torquay earlier this year.
Johnson said: "He is not part of my plans, it's that simple.
"It would be rude to go into details and I won't do that."
Source: PA
Source: PA