The world number four missed out by a single shot at Baltusrol after only managing to add a second-round 69 to his opening 74.
McIlroy claimed that his approach play was as good as anyone else's over the two rounds, but described his putting performance as "really disheartening".
"Tee to green was good, but it was just pathetic when I got onto the green. I just need to do a lot of work. Putting let me down at Oakmont and then putting let me down here again. My tee to green game, there's not much wrong with that. It's pretty solid," he told reporters.
"I think if you had given anyone else in this field my tee shots this week, they would have been up near the top of the leaderboard. It just shows you how bad I was around the greens. I was planning on taking two weeks off and then practising the week before Barclays. I'll still take two weeks off from tournaments, but I'll have to see what my practice schedule looks like.
"I need to do something...I just need to figure out what to do on the greens. I need to have a long hard think about that. I've hit the ball really well this week and I'm walking away not playing the weekend. It's really disheartening. As I said, I need to go back to the drawing board and see where we go from here."
McIlroy, who also missed the cut at the US Open in June, won the US PGA in 2012 and 2014.