Kisner, the 33-year-old from South Carolina, had set an imposing clubhouse target at the PGA Championship of eight-under 134, but on a day hit by a thunderstorm, Matsuyama joined him on that mark.
A near two-hour delay held up the later starters, but when play resumed Matsuyama secured two more birdies to match the American.
He is coming off a fine win at the WGC event at Akron last week and has carried over that form with immaculate play from tee to green.
In draining, humid conditions, Matsuyama admitted the delay may even have helped him. "I was able to lay down in the locker room and get some rest," said the 25-year-old rising star of world golf.
Jason Day of Australia, the former champion and world number one, is the closest challenger to the leaders, finishing off a brilliant second round 66 in near darkness. An eagle-birdie-birdie run before the storm was the highlight and left him two back on 136.
Italy's Francesco Molinari, who also carded a 64, and Louis Oosthuizen of South Africa shared fourth, a shot further back.
Much earlier, Kisner, who held the first round lead with Dane Thorbjorn Olesen, picked up where he left off Thursday evening, hitting 15 of 18 greens in regulation to make three birdies and an audacious eagle on the seventh, where he holed a monster putt.
A single bogey on the 13th was the only blemish on his card and Kisner, who claimed the prestigious Colonial title, combined with two other runner-up spots on the PGA this season, feels he is on a roll.
"I'm hitting the ball really nice and things are going my way," he told the official PGA Tour website. "Hitting the fairway here is the key and I'm making a lot of putts."
While Kisner prospered, Rory McIlroy's bid for a fifth major title foundered as he dropped four shots in the space of five holes having moved into contention on his front nine.
In danger of missing the halfway cut for the fourth time in seven majors, the Northern Irishman battled back with two straight birdies and nearly made it a hat-trick when his putt on his final hole teetered on the cup but did not drop.
Despite trailing the leader by 10 shots, McIlroy still feels he is in with a chance of victory in the final major of the season.
"Obviously Kis (Kisner) is on fire right now. But take him out of the equation, I feel like I'm still right here in the tournament," he told the UK's Press Association.
But having shot previous rounds of 61 and 62 at the course in North Carolina, McIlroy conceded that the revamped 7,600-yard layout was a very different proposition. "It surprised me," the 28-year-old admitted. "I'm not surprised to see so many guys over par."
Jordan Spieth, seeking his career grand slam after winning the British Open last month, also struggled, with a second round 73 leaving him at three over, 11 behind the joint leaders.
The new Quail Hollow has certainly proved too tough a test for some of golf's elite, with Phil Mickelson the most notable victim in his 100th appearance at a major championship.
After his first round 79, "lefty" was always struggling to make the cut and a three-over 74 sealed his fate, with the five-time major winner failing to make a birdie until his 31st hole.
It It is the first time the 47-year-old has failed to make the weekend play at the PGA Championship for 22 years.
"Its not like I'm hitting the ball crooked, I'm just hitting it in the wrong spots," was Mickelson's verdict on his performance.
Defending champion Jimmy Walker also missed out, bravely following a disastrous first round 81 with a battling two-under 69, but still way outside the projected cut mark of four over.
A total of 26 players were unable to complete their rounds, including American Chris Stroud at five under with five holes to play.