The 27-year old left-back has not played for the Seasiders since returning from Australian national team duty at the end of March and has been restricted to just 11 appearances for the club this season.
Carney’s shoulder problems go back to his days at Dutch club FC Twente and arose again when he was playing for the Socceroos at the Asian Cup in Qatar in January.
The former Sheffield United man insisted that he was now looking forward to being right for pre-season.
"I saw the specialist the other day and he just said he recommends that I should get it done," Carney told the club's official website.
"I was testing it out and it's not good - I think there is a bit of bone damage there, so it just needs fixing and hopefully I will be back for pre-season next year."
Ian Holloway’s men meet bottom-of-the-table Wigan Athletic in a must-win match at Bloomfield Road this weekend.