Austin dislocated his shoulder in training last week and is set to undergo surgery on the problem.
“Charlie dislocated his shoulder in training this week and is due to go under the knife on Wednesday to have an operation to sort the problem out,” Burnley manager Eddie Howe told the club’s official website.
“He will be out for the season but should be back as good as new for the first day of pre-season.
“It’s really bad luck for the lad because we’ve all got high hopes for him here. But he is one for the long term and we have to take the long-term view on it and protect him by getting the operation done now and getting him right for next season.”