The club confirmed to AFL.com.au on Sunday that Clarke had surgery to repair medial ligaments in his right knee after playing out most of the season in significant pain.
The 24-year-old managed 21 games this season, including two finals in which his performance was sub-par.
Clarke missed the start of the season after injuring his knee at a music festival.
He had also missed the start of the 2013 season with a calf injury.
Meanwhile, North Melbourne expects forward Drew Petrie to be fit for day one of pre-season after he underwent ankle surgery.
Petrie had the ankle joint cleaned out earlier this month but was reportedly back at the club's headquarters last week.
He's set to play alongside Carlton recruit Jarrad Waite in 2015 in a tall Roos forward line.
