The 29-year-old German, three ahead of the chasing pack after opening with a five-under-par 65 that he described as "exceptional", birdied four of his first 13 holes under sunny skies to move to nine under for the tournament.
That left him six strokes in front of his closest pursuers, burly Zimbabwean Brendon de Jonge and long-hitting American Dustin Johnson.
De Jonge, who had carded a 68 on Thursday, was one under for the day after 15 holes while Johnson, who opened with a 69, was two under for his round with four holes remaining.
Northern Ireland's Graeme McDowell, the 2010 U.S. Open champion at Pebble Beach, and American Kevin Na were at two under for the tournament but yet to start the second round.
Kaymer, who gained a major confidence boost from his victory at the elite Players Championship last month, has played near-flawless golf at challenging Pinehurst over the last two days in the year's second major.
His opening 65 included six birdies and a lone bogey and the former world number one was error-free for his first 13 holes on Friday.
With barely a breath of wind on Pinehurst's fabled No. 2 Course which was softened by 0.64 inches of rain overnight, Kaymer birdied the 10th, 13th and 16th to reach the turn in three-under 32.
Seeking a second major title after clinching his first in the 2010 PGA Championship, he picked up another shot at the par-four third to forge six ahead of the chasing pack before parring the fourth.
World number one Adam Scott, who had struggled with his short game on the way to an opening 73, was two under for the day after 13 holes but a distant 10 strokes behind Kaymer.
(Reporting by Mark Lamport-Stokes; Editing by Pritha Sarkar)
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