It leaves him six shots off the lead.
Shane Lowry added another feather to his cap this morning as he became an Olympian.
He took to the course in Japan in the early hours of this morning alongside Tommy Fleetwood and Patrick Reed.
It was a superb start with a birdie on the par four 2nd hole and the former Open Champion continued steadily with nine straight pars.
A bogey on the 456 yard, 12th hole will be disappointing but once again the Clara man's mental strength came to the fore as he made a second birdie of the round on the par three 16th.
There was a delay in the middle of the round due to stormy weather and the potential of lightening at the Kasumigaseki Country Club which may have helped Lowry regain his composure for a final push.
McIlroy has signed for a two-under-par round of 69 and will also have work to do on day two.
Austria's Sepp Straka has a one-shot lead at eight-under.
He is back on the course tomorrow morning after 4am Irish time.