Allen, who pulled out of the Wales squad for their World Cup qualifiers against Scotland and Croatia on Monday, will have an operation on Thursday in an effort to be fit for the start of the next Premier League campaign.
"Joe Allen is due to have a left shoulder operation tomorrow morning in Liverpool and will be ready to return to football at the beginning of next season," Liverpool first team doctor Zaf Iqbal said.
The 23-year-old midfielder suffered a recurrence of the injury in October and has played through the pain barrier since.
The injury has not improved and he was substituted at halftime in Saturday's 3-1 league defeat at Southampton.
Liverpool, seventh in the standings, have slipped out of the running for the Champions League spots, trailing fourth-placed Tottenham Hotspur by nine points with eight games to play, but still have a slim chance of qualifying for the Europa League.