The Northern Ireland international left the pitch on a stretcher and wearing a neck brace following a clash of heads during Wednesday's 3-1 win over Dunfermline at Ibrox.
The forward has been taking to hospital, believed to be the nearby Southern General, where scans will reveal the full extent of the injury.
McCoist said: "He doesn't look good. I'm going up to the hospital to see him.
"I spoke to the doc, and it's guess work because he's not been X-rayed yet, but it looks a really bad one in terms of a compressed or depressed fracture of the cheekbone.
"That's what it looked like. It was a really sore one."
Asked about the potential timescale if Little has suffered a fracture, McCoist added: "It would be months. I don't know because I don't know the severity of it."
McCoist is also sweating over the fitness of defender Richard Foster, who limped out of the action with an ankle injury.
The Light Blues boss said: "I'm not sure the chap who did that particular tackle was even spoken to.
"Foster has got a bad one. He is in there on crutches.
"We will have to re-assess it tomorrow and he will probably need an X-ray.
"I'm hopeful it's not as bad as it looks at the moment.
"It was perhaps another incident where the referee could have taken more severe action."
In what proved to be a bruising encounter, Lee McCulloch was also forced out of the match for a 15-minute spell to receive stitches in a head wound.
McCoist said: "He got six stitches which took a whole lot longer than I was hoping for to be honest with you.
"But the skipper is the skipper and his main objective was to get back on the park.
"Thankfully he did and led us to another great victory and converted the penalty with aplomb."
McCulloch opened the scoring from the spot with 20 minutes to go, with Jordan Moore - who McCoist felt was lucky to escape a red card for the earlier challenge on the skipper - dismissed for conceding the foul in the box.
Jon Daly then doubled the advantage and Josh Falkingham pulled a goal back for the Pars, before Bilel Mohsni sealed a 3-1 win in injury time.
McCoist said: "I have to say that I thought we deserved the victory.
"We scored two very good goals and a penalty. We were a bit sloppy at the goal we lost.
"The second half was better than the first half and thankfully we took our chances."
Dunfermline boss Jim Jefferies was unhappy with the penalty award and the red card.
He said: "I don't think they broke us down at all until they got the penalty, which was a very soft award.
"A young boy of 20-years-old throwing Lee McCulloch about? I don't believe it.
"It was a blow for us. But I'm proud of every one of them.
"They are a young team, with no experience at this level at all and they gave a great account of themselves."
- Sports & Recreation