The England international suffered a dislocated shoulder on Sunday in Burnley’s 1-0 win over Crystal Palace at Turf Moor.
Heaton had to leave the field in the first half after landing awkwardly when going up to claim a high ball and boss Sean Dyche admitted after the match that he feared the worst.
The stopper was taken to hospital for further assessment and he has now gone under the knife to correct the issue as swiftly as possible.
Number two Nick Pope is set for an extended run in the starting eleven with Heaton expected to be sidelined for at least a few months, while Adam Legzdins will provide backup.
Reports claim that Dyche is also considering a move for free agent Anders Lindergaard as he looks to ensure he has enough cover.