Brooker signed for Doncaster in January this year, but has been fighting to recover from a calf tear suffered in training and has made just one appearance for Rovers.
Specialists have revealed that an unstable ankle could be the root of his injury problems over the last year and the 28-year-old could undergo surgery before returning to full fitness.
"He's got quite an unstable ankle which you would only find if you were actually testing for it," manager Sean O'Driscoll told the club's official website.
"That seems to be the cause of all his problems. He's with the specialists at the moment and I think we'll make the decision to sort it out once and for all.
"It's quite a routine operation, but it does mean that he's out for the rest of the season."