The Manchester United defender is not expected to return until the early stages of next season.
"Matthijs de Ligt has undergone successful surgery to address a back injury," United said in a statement on Friday.
"Having diligently worked throughout his rehabilitation process, the decision was made that a corrective procedure was the best course of action."
De Ligt had made a positive start to this season, playing every minute of United's first 13 Premier League games until the injury halted his progress.
"Since November, I have done everything, pushing myself in every session and exploring every option, to get back to doing what I love, playing football," said the former Juventus and Bayern Munich centre-back.
"I am grateful to everyone who has supported me throughout a difficult period in my career.
"I remain as determined as ever to represent Manchester United and play in front of our incredible supporters as soon as possible."