The British world number nine, who missed the cut in last week's Players' Championship on his first appearance since winning the year's first major, dropped only one shot at the K-Club on the outskirts of Dublin.
Four-times major champion McIlroy, the world number three, birdied the 18th at his home Open to complete a round of 67, one shot ahead of young Briton Callum Shinkwin and South African Jaco van Zyl.
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The 28-year-old Willett's round of 65 was only one shot off the course record set by South African Charl Schwartzel in 2003.
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