McIlroy aggravated the injury at The Players Championship last week in Florida where he earned a share of 35th after finishing two over par at TPC Sawgrass.
"Having had a reaction to my earlier rib injury, I have been advised to take a conservative approach to my recovery which unfortunately means I have to withdraw from the BMW PGA Championship next week," McIlroy, who won the event in 2014, said on the European Tour's website.
"It's a disappointing decision to have to make, but I have to ensure I make a full recovery. I will now continue the process of preparing my game for... the rest of the season."
(Reporting by Frank Pingue in Toronto, editing by Pritha Sarkar)
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