Koekkoek came out of the midget ranks having attended prep school with the Notre Dame Hounds, which is the same program that developed future Lightning stars Vincent Lecavalier and Brad Richards. After posting 16 goals and 43 points in 44 games for the Hounds in 2009-2010, he was selected by the Peterborough Petes in the 1st round, 7th overall, of the 2010 OHL Priority Draft.
He struggled on a very young Petes team in 2010-2011, posting a -29 rating in 65 games. Still, his 7 goals and 23 points in the campaign were good enough to earn him a Second Team OHL All-Rookie selection. He also earned his way onto Canada's U18 World Junior Championship team where he posted a modest 1 goals and 2 points in 7 games.
Koekkoek had seized the mantle of Peterborough's top defenseman and minutes eater in the first half of 2011-2012, but a season-ending shoulder injury cut short his year after 26 games, in which he had 5 goals and 18 points. He was rated #23 among North American skaters by the NHL Central Scouting Service prior to his selection in the 1st round, 10th overall by the Lightning at the 2012 NHL Entry Draft.