Thirlwell limped out of the 2-1 defeat to Hereford on Tuesday after aggravating a calf injury and could miss out.
Defender Ian Harte is also in line to make his debut after joining the club on a deal until the end of the season.
Player/coach Graham Kavanagh is hopeful of facing the Cobblers despite struggling with a knock to the hip he sustained against Hereford.
Defender Peter Murphy is a doubt once again with a groin injury, while striker Kevin Gall has returned from his loan spell with Port Vale but is out for up to three weeks with a calf injury.
New signing Jared Hodgkiss could make his debut for Northampton.
The 21-year-old full-back joined the Cobblers on loan from West Brom on Thursday and is set to go straight into Stuart Gray's squad for the game against the Cumbrians.
But Adam Watts, another deadline-day recruit from Fulham, may have to wait for his debut until he is fully recovered from a bout of concussion.
Gray will assess the fitness of defenders Chris Doig and Jason Crowe before naming his side. Skipper Doig missed the relegation-threatened Cobblers' 4-3 home defeat against Swindon on Tuesday night with an Achilles injury and Gray revealed it is "touch and go" whether he will play any part.
Crowe is struggling with a groin injury and Gray will be keeping his fingers crossed that he is passed fit.
On-loan striker Scott Vernon could be handed a start alongside Adebayo Akinfenwa for the first time since his move from Colchester, while midfielder Ryan Gilligan remains on the sidelines with a knee problem.
Sporting Life