The 23-year-old has been troubled by a shoulder injury since November last year, and he aggravated the problem in Saturday's 3-1 defeat at Southampton.
Allen was withdrawn from the Wales squad ahead of their World Cup qualifiers against Scotland and Croatia, and it has been revealed that he will undergo surgery on his left shoulder on Thursday.
He faces a recovery period of around three months after the surgery, and Liverpool were keen for him to have the procedure as soon as possible to enable him to be fit for the start of next season.
Liverpool first-team doctor Zaf Iqbal said: "Joe Allen is due to have a left shoulder operation on Thursday morning in Liverpool and will be ready to return to football at the beginning of next season."
Allen's first-team appearances have been limited after Lucas Leiva returned from injury, but the former Swansea ace refused to blame his dip in form on his injury in an interview with the Liverpool website last week.
"I've had an operation in the past and unfortunately I've had a recurrence of the injury and carried it for a little while," he said. "Recently, in particular, it has deteriorated and we have got to a stage where we have to do something about it.
"It's something I've been able to play with, though, so there are no excuses in that department."