Despite a couple of early birdies, the Northern Irishman found himself one-over for the day at the turn.
Things got a lot worse as he moved down the back nine as his wayward approach shots cost him a double-bogey at 10 and bogeys at 11 and 13.
As his round drew to close though, McIlroy just about made the cut at four-over, holing a five-footer for par on the final hole.
Elsewhere, defending champion Adam Scott remained in contention despite three bogeys in his first five holes.
The Australian found his putting rhythm on the back nine to claw back those three shots and remain on three-under at the halfway stage.