The 22-year-old Northern Irishman followed up his opening round of 65 with five birdies and an eagle for a superb 66 to reach the halfway stage at 11-under-par 131.
His total shaved one stroke off the previous US Open record of 132, set by Ricky Barnes at Bethpage two years ago, and was just one off the lowest halfway score at any major, the 130 set by Nick Faldo at the 1992 British Open at Muirfield.
"It's been very, very good," McIlroy said in a televised interview. "It's very near the best I can play." McIlroy's round could have been even better had he not made a double-bogey six at the final hole after hitting his approach into the water.
He had became the fastest player ever to reach double digits under par at a US Open when he holed out from the fairway at the par-four eighth, his 26th hole, for eagle to reach 10-under.
He also birdied the 14th and 16th holes before rolling in a 12-foot putt at the par-four 17th to push his total to 13 under par, surpassing the record low mark of 12-under, set by Gil Morgan during the 1992 US Open and matched by Tiger Woods when he won the 2000 championship at Pebble Beach.
But McIlroy spoiled his flawless start to the championship when he found the water with his approach to the 18th after finding the left rough off the tee.
"Naturally, you've got to be disappointed after walking away with a six but looking at the overall picture over two days, I feel very good," he said.
"I have to keep it going over the next two days. I'm only halfway there." Yang Yong-eun of South Korea, the first Asian man to win a major with his victory at the 2009 PGA Championship, was a distant second.
Yang was at three-under-par following his opening round 68 and was about to tee off in the afternoon wave when McIlroy finished.
In the clubhouse, on two-under-par 140, were Spain's Sergio Garcia, who shot even-par 71 Friday, American Robert Garrigus (70) and former Masters champion Zach Johnson (69).
McIlroy, showing no signs of nerves after blowing a four-stroke lead at the Masters two months ago, played free and easy as he put himself in position to win his first major after finishing in the top three in three of the last six majors.
"It's a big challenge but everytime I get myself into the position it feels more natural every time," he said.
