The 28-year-old, who has been troubled by his shoulder in the past, was forced off in the first half against Watford because of the problem and, after having the injury assessed by surgeons, it was found that the damage was more serious than first thought.
"Darren Pratley will be missing until the end of the season," revealed Wanderers boss Dougie Freedman.
"He was still feeling a complaint. They went into his shoulder and the surgeon found bits of screw had snapped off all over it. He had to take them all out and restructure his whole shoulder."
It is the second bit of bad news Wanderers have received on the injury front this week following the luckless Stuart Holden's latest knee problem.
The Sky Bet Championship club are awaiting to hear back from scans on Holden's knee but fear he may have suffered another serious problem.