The 25-year-old midfielder has not featured since late November due to knee and hamstring issues.
Doncaster Rovers boss Gary McSheffrey had hoped to see the summer signing return to full training later this month.
However, Close opted to go under the knife this week after it became evident that his knee was not healing as he hoped.
"He had something called a runner’s knee. It’s an IT band syndrome on the outside of his knee.
"He’s done everything to try and avoid surgery like going to see specialists and having injections down in London – he’s been to see the top guys – but it’s just not cleared up and it’s still sore when he runs.
"The IT band needed lengthening so he’s had surgery yesterday and that’s a 12-week rehab. He’ll get fit for pre-season.
"It’s a big blow and I was looking forward to hopefully having him back within the next couple of weeks. It’s disappointing but his fitness and his welfare is the most important thing.
"He tried to do everything to get fit without surgery but ultimately Ben felt that surgery was his only option now to clear it up and we go with his decision and what he wanted to do.”