The British Open champion, in pursuit of a third consecutive victory on the PGA Tour, fired a four-under-par 67 on a wet, ultra-long Valhalla layout where play was suspended for 45 minutes earlier in the day due to water-logged conditions.
McIlroy, the pre-tournament favourite heading into the year's final major, holed out for eagle from 30 feet in front of the green at the par-five 18th and also recorded four birdies and two bogeys to post a nine-under total of 133.
He squandered a golden opportunity to add another eagle at the par-five seventh, where he hit a stunning second shot from 243 yards to just eight feet before missing the putt, but signed off with a birdie at the ninth where he drained a 16-footer.
That left three-times major winner McIlroy two strokes in front of American Ryan Palmer, who birdied his last two holes for a 70 after teeing off in the first group of the day in heavy, driving rain.
"I wasn't sure we should have teed off when we did," said Palmer. "I could barely see the fairway on one.
"Fairways are not rolling at all. You are going to need a lot of mid to long-irons. Even par is a good round today, so it's nice to get under par."
England's former world number one Lee Westwood and American Kevin Chappell, who had been tied for the overnight lead with Palmer after opening with 65s, were both at six under after completing just one hole in the second round.
Fourth-ranked Swede Henrik Stenson (71), veteran American Steve Stricker (68) and Canada's Graham DeLaet (68) were knotted at five under, three strokes off the pace.
McIlroy, however, commanded the spotlight as he lived up to his pre-tournament billing with another consummate display in often difficult conditions after making a scrappy start.
Initially struggling for accuracy off the tee, he dropped a shot at the par-four 12th where he found a bunker with his approach, but swiftly responded by sinking a 12-footer at the 13th and a 16-footer at the 15th to get to six under.
Though the 25-year-old Northern Irishman squandered another birdie chance at the 16th, where he missed an eight-foot putt, he reached the turn in sizzling style with his eagle on 18.
McIlroy dropped another shot at the par-four second, where his tee shot ended up in the rough and his second in a bunker, but maintained his grip on the tournament with two birdies in his last three holes.
Veteran Stricker, who has played a limited schedule on the PGA Tour for the past two years, surged into contention with four birdies on his front nine, capped by a 30-foot putt at the 17th.
Out in four-under 32, Stricker made his only bogey of the day where he found two bunkers en route to the green before finishing his round four strokes off the lead.
The cut was projected to fall at even par, leaving players such as four-times winner Tiger Woods with ground to make up if he is to advance.
Woods, tournament rusty after having surgery in late March to treat a pinched nerve in his back, struggled to opening 74 on Thursday and parred his first hole on Friday to remain at three over.
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