He birdied three of his final four holes, and had an eagle, five birdies and two bogeys to match his lowest PGA Tour round this year.
With a birdie on No. 18, McIlroy reached 7 under to break out of a four-way tie for the lead.
"It's nice to see my name on that part of the leaderboard," McIlroy said. "It's obviously even nicer to be leading and have a great chance."
Jeff Maggert, tied for the first-round lead with John Merrick, shot a 68 to match J.B. Holmes (64) and Kevin Stadler (65) at 6 under. Merrick had a 69 to join Chad Campbell (67) and Kevin Kisner (66) at 5 under.
Davis Love III, the Americans' Ryder Cup captain, had a 68 and was tied with Padraig Harrington (68) at 4 under. John Daly birdied his first three holes on his back nine to get to 5 under but finished with a 69 and was at tied at 3 under making his fourth cut in five events.
No one has ever won a PGA Tour event, then followed up the next week by winning the US Open. After playing only two rounds each at The Players Championship, the BMW PGA Championship in England and then the Memorial last week, McIlroy isn't thinking about history. His goal in Memphis is playing as much competitive golf as possible while honing his game.
"I saw a lot of positive signs with my ball striking. Hit a lot of good iron shots and drivers. So that was something that I was really working on the last couple of weeks and feels like it's coming together for me. So excited to be in this position for the weekend. This is really what I wanted heading into next week," McIlroy said.
"For the time being, my mind is focused on trying to win this golf tournament."
McIlroy certainly has his driver working well. Even when his caddie suggested a 3-wood off the tee at No. 18, McIlroy stuck with his driver and drove the ball 329 yards. That left him 115 yards to the pin, and he hit his approach to 5 feet for the final birdie and the lead.
He started four strokes back of Holmes, who took advantage of a morning tee time to take the clubhouse lead at 6 under. McIlroy moved into a three-way tie atop the leaderboard with his second birdie of the round on the par-3 11th. He stuck his tee shot 5 feet from the hole and rolled the putt in for birdie to reach 6 under.
He bogeyed Nos. 12 and 13 to fall back. McIlroy said he wasn't happy that he had a wedge in his hand in the fairway on No. 13 from 127 yards only to hit into the rough turning a birdie chance into a bogey.
McIlroy turned it around on the par-5 16th, hitting his second shot to 4 feet. The ball hit the left edge and curled right, leaving McIlroy to tap in for birdie and a share of the lead. He had a nice par save on No. 17 after hitting his drive behind a tree and his second into a greenside bunker before getting up and down with a 4-footer for par and the final birdie.
"To finish strong the way I did was great, and it gives me momentum going into tomorrow," McIlroy said.
Holmes had his low round of the year as he works his way back from brain surgery last September. He had seven birdies and a bogey, putting himself into strong position.
"I wasn't knocking pins down, but I hit them in there pretty close," Holmes said. "Made a couple 6-footers, but I putted well. I was hitting it 15, 20 feet and making some putts."
Meanwhile, on the Nationwide Tour, Manawatu professional Tim Wilkinson shot a five under par 67 at the Mexico Open to climb 40 places at the El Bosque Golf Club.
The former PGA Tour player, who opened with a one over par 73, bounced back in fine style to get to a four under par total and now sits within five shots of leader Tag Ridings of the United States.
Wilkinson, who is currently 56th on the Nationwide order of merit, played the front nine in one under par and the back nine in four under in a bogey free performance.
Hamilton professional Steven Alker, who opened with a two under par 70, shot a one under par 71 to be one shot further back in a tie for 24th place.
Tauranga professional Josh Geary missed his fourth cut from as many events in 2012 on the Nationwide Tour. The Kiwi, who finished third at the New Zealand Open, shot rounds of 78 and 79 to finish at the bottom of the field in a share of 135th place.
On the European Tour, Lee Westwood kept the chasing pack at bay to maintain a three-shot lead going into the final round of the Nordea Masters in Stockholm.
A day after carding a stunning 64, a round of 68 was good enough for the world No.3 to maintain the advantage he enjoyed at the halfway stage at Bro Hof Slott Golf Club.
Westwood finished the day on 16 under, with fellow Englishman Ross Fisher second at 13 under after a superb 65.
-AAP