The world number four had opened with a 72 on Thursday to give him a halfway total of one over par, well outside the projected cut of 2 under.
This would be the fourth time in five years McIlroy has missed the cut at the Irish championship. The odd year is 2016 - when he not only made the cut but won the tournament.
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"I felt like I was battling well, two under through 13 and with another par five coming up, and to bogey the sixth took the wind out of my sails," said McIlroy, who showed his frustration by slamming his driver to the ground after a poor drive at the 16th.
"My short game, in general, it's just silly mistakes," he said. "I'm just not being very efficient with my scoring and that's why I'm making it difficult for myself. Just need to tidy up the short game a little bit; I feel like the long game is there."
McIlroy will compete in next week's Scottish Open before heading down to Royal Birkdale for the British Open.
"Obviously, I might have a few commitments here this weekend, but I need to practice," he said. "I need to get sharp and get ready for next week and ultimately for The Open in a couple week's time."
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