Barker pulled-up with a hamstring strain 25 minutes into the 1-0 victory.
He looked distraught when turning towards the North End bench to signal that he couldn’t continue.
It is the latest in a list of injuries to hit the PNE squad of late.
If Barker’s injury is of any length, it will leave Neil shy of another attacking player.
In his preferred 4-2-3-1 formation, the attacking line behind the striker has been particularly badly hit.
Billy Bodin, Josh Harrop, and Callum Robinson are all already long-term absences.
Sean Maguire has played wide too but is expected to be out until January.
With Barker, it is a wait-and-see scenario for how long he will be out.
Post-match at Forest, Neil said: “It is a hamstring.
“It is too soon to say how long he’ll be, we will have to assess him.”
Barker, on a season’s loan from Manchester City, has had hamstring issues during his career.
After last month’s 1-1 draw with Middlesbrough, Barker spoke about how four times earlier in his career he had suffered a hamstring tendon injury similar to the one which had recently ruled out his team-mate Robinson.
To cover his early exit at Forest, Tom Barkhuizen came across to the left-wing and substitute Lukas Nmecha played on the right.
The shortage in attack is something Neil will have to battle through until January when the transfer window opens for business.
Against Forest, Neil was at least able to welcome back Daniel Johnson from injury far sooner than expected.
Johnson made it back a month early and played until well into stoppage-time.
In the back four, Tom Clarke and Ben Davies both returned from injury.
Clarke played wearing a mask to protect his broken nose, with Davies back from a hamstring niggle.
But a thigh strain ruled Josh Earl out, that handing a return to Andrew Hughes at left-back.
Ben Pearson didn’t make the trip to Forest because of a thigh injury.
The talisman midfielder has been making progress in his recovery but Saturday came too soon for him and he was not risked.
It will be hoped Pearson can return for Millwall’s visit to Deepdale this weekend.