Nick Pope, who was part of England's squad at the World Cup in Russia, suffered a dislocated shoulder in last week's first leg of the Europa League second qualifying round tie against Aberdeen which ended 1-1.
Burnley manager Sean Dyche said that Pope had undergone a operation on his shoulder but that there was no timescale for his return.
"He's had the op. So far it's pleasing news in the sense the specialist was happy," said Dyche.
Tom Heaton, who missed most of last season with his own shoulder injury, was expected to start against Aberdeen but has been sidelined with a calf injury.
Danish keeper Anders Lindegaard came on as a substitute in the first leg in Scotland and is expected to start on Thursday.
Burnley's fourth keeper is former Derby County custodian Adam Legzdins, who has not been registered for UEFA competition.
Teams had to submit a list of players to UEFA for European competition before the tie began.
(Reporting by Simon Evans; Editing by Christian Radnedge)
