Seven players were tied at the top after a damp day at the Quail Hollow Club.
McIlroy won this event three years ago and has gone on to capture two major championships. He led both the PGA Tour and European Tour in earnings last year, but struggled early this season.
After finishing second at the Texas Open in an apparent sign he had his game in working order, he needed a 3-under 69 in the final round just to finish tied for 25th at the Masters.
Phil Mickelson, Boo Weekley, 2011 champion Lucas Glover, Zach Johnson, Kevin Streelman and Jason Kokrak were all tied for eighth at 68. Mickelson was the runner-up in this tournament when McIlroy won it in 2010.
Among those tied for 14th at 69 were rookies Jordan Speith and Russell Henley. There were 22 players within two shots of the lead.
McIlroy's round was highlighted by a stretch of six birdies in seven holes beginning at the par-5 sixth.