Gilligan - who opened the scoring in the Cobblers' 4-1 thrashing at Prenton Park earlier this season - was forced out of the abandoned clash with MK Dons on Tuesday with a knee injury.
Gray said: "He's got a slight cartilage twinge which we have been trying to manage over the last few weeks. He forced his knee back on Tuesday so he has missed training but there is a chance he may be available."
Captain Chris Doig will again miss out with a one-game suspension after the match with MK Dons was abandoned at half-time due to torrential rain, while striker Adebayo Akinfenwa will serve the second of a four-game ban.
Wing-back Liam Davis is back in training after a hernia operation and could come into contention while midfielder Luke Guttridge is also close to a return from his knee problem.
Tranmere boss Ronnie Moore could hand a debut to on-loan Preston winger Danny Mayor.
The 18-year old signed his first professional contract with Preston in December and has impressed in their reserve side this season.
He has joined Rovers on a one-month loan and defender Ian Goodison is hoping to return after serving a one-match suspension in the 2-1 defeat at Hartlepool in midweek.
However, Goodison is also nursing a knock and will be assessed along with a number of other players.
Full-back Ryan Shotton missed the Hartlepool with a groin strain while Terry Gornell (stomach) and goalkeeper Danny Coyne (medial ligaments) are also nursing injuries.
Striker Bas Savage (foot) looks set to be missing and fellow frontmen Craig Curran (back and stomach) and Chris Greenacre (foot) definitely miss out.
Sporting Life