McIlroy finished the day 12-under-par 130 at the TPC Boston.
Playing the front nine second Saturday, McIlroy bogeyed the par-5 second hole as well as the par-3 third.
But the world No. 1 rebounded with birdies on the fourth and fifth thanks to some clutch putting.
Louis Oosthuizen also fired a 65 to gain sole possession of second place at minus-11.
Tied for fifth at minus-9 were first-round leader Seung-Yul Noh (even-par 71), Jason Dufner (66), D.A. Points (65), Charl Schwartzel (65) and Chris Kirk (70).