Harper is expected to return to full training in six weeks.
North Melbourne's director of football, Geoff Walsh, told the club's website that the Kangaroos always thought Harper might require a procedure to follow up from surgery he had in October to de-bride scar tissue following a high grade traumatic ankle injury.
"We always knew there'd be a chance of a follow-up procedure with Kieran before the start of the season,' Walsh said.
"We managed to get some significant work into him following the Christmas break, but in order to allow him to reach his full potential this season and beyond, the time was right for Kieran to undergo this additional procedure."
The 21-year-old played played 37 games in his first two seasons but just three in 2013.
He was dropped after round three and injured his ankle playing in the VFL with Werribee.
Harper also had a minor operation on his elbow at the end of last year.
