The 32-year-old, who moved to the Sixfields Stadium on a free transfer from Premiership side Birmingham City back in November, has damaged his cruciate knee ligament and will have an operation to treat the injury on Friday.
Gill was initially earmarked last week as one of ten players to leave the club in the summer but manager Martin Wilkinson has decided that he will look to offer him a contract extension.
Cobblers boss Wilkinson is hopeful to have Gill back fit by November, when the club will be well into their new season in Division Three.
"Jerry has a serious injury," Wilkinson told the Northampton Chronicle & Echo.
"He has damaged his cruciate knee ligament but we are hoping he will be fit by around November.
"He is due for an operation on Friday but we do want to look after him however we can.
"We feel a moral responsibility and we will see what we can do.
"We want to look after the players who have looked after us and he has been one of the more positive and hardworking players we have had in a difficult season."
Meanwhile, The Cobblers are interested in taking Hull City striker Lawrie Dudfield permanently from his parent club Hull City.
The 22-year-old is currently on loan at The Sixfields and both clubs are in talks regarding a possible summer move.
