Keith Cowan was taken to Letterkenny University Hospital immediately after he was stretchered off around an hour into Tuesday night's game against St. Patrick's Athletic.
The early indications were that the defender suffered a serious knee injury.
Speaking after the game, his manager, Ollie Horgan, said Cowan won't play again this season.
“It was a great result but we probably paid a heavy cost with the injury to Keith Cowan,” Horgan said.
”Keith has damaged his knee. He has been taken to the hospital. Hopefully there’s no break in it, but I think we’re more worried about ligament damage around the knee cap.
“Certainly his season is over, it could be a bit longer than that,” he added.
“He’s a massive loss to us. To be fair to him, he was probably our most consistent player, through the bad days as well as the good days. But certainly in the bad days, he stepped up to the standard and he’ll be a sore loss for the remainder of the season, if not longer.”