The 28-year-old damaged the bone in his left ankle during training last Sunday (AEDT) and subsequently missed the 1-1 Premier League draw with Newcastle United.
The club confirmed in a statement on Thursday that Boly is set to be sidelined for some time, although they have not discounted a possible return this season.
Wolves head of medical Phil Hayward said via the club's website: "Willy had surgery in London this morning to repair the bone with a small metal plate and screws.
"The procedure went as planned with no complications and he will now return to Compton to begin the early stages of his rehabilitation.
"Willy will be in a boot for the first six weeks, working hard to maintain fitness and muscle bulk in the leg before progressing to more functional activities.
"In terms of time scales, a lot depends on how he progresses in the first few weeks and how well the fracture heals."
Boly has made 16 appearances in the Premier League and Europa League this season and scored the only goal in a 1-0 win at Besiktas earlier this month.