The 2023 US Open champion returned early on Friday to complete the final two holes of his opening-round 64 after fog delayed play on Thursday. He then followed it up with a steady second round 69 that featured three birdies and two bogeys, capped by a lengthy birdie putt on his final hole.
"The great thing about that is I didn't feel like I had my best and I still am leading," Clark said. "Hopefully I can bring my A-game on the weekend."
Clark's seven-under total leaves him four shots clear of Xander Schauffele, who climbed into a share of second place alongside 2022 US Open winner Matt Fitzpatrick and American Sam Stevens, while Collin Morikawa sits one stroke further back after matching the day's lowest round with an impressive five-under 65 in difficult conditions.
Rory McIlroy briefly threatened to mount a challenge after reaching the turn in three-under 33 and closing within four shots of Clark. However, his momentum faded on the back nine as he mixed two birdies with three bogeys and a costly double bogey to sign for a one-over 71.
McIlroy's challenge unravelled after the turn when wayward approach shots at the 10th, 11th and 12th led to three consecutive bogeys. He responded with birdies at the 13th and 14th, including a spectacular 40-foot putt, but fell back to level par after a double bogey at the par-four 15th.
"I just kept hitting it long," McIlroy told Sky Sports. "It was tough. I feel like our side of the draw played in the windiest of the conditions and the scores sort of bear that out, but I held in and hung in there as best I could.
"Even par going into the weekend isn't terrible. Hopefully go out there and keep playing the way I'm playing. I'm doing the right things. I made a couple of mistakes, which put me behind the eight ball a little bit, but still a really solid two days."
McIlroy heads into the weekend on level par alongside World No 1 Scheffler, who produced a second-round 68 as he continues his pursuit of the career Grand Slam.
Elsewhere, two-time US Open champion Bryson DeChambeau failed to make the cut, marking his third successive missed cut at a major championship.
Jon Rahm also missed the cut when he dropped six shots in a five-hole stretch during an eight-over 78, while Viktor Hovland, Patrick Reed, Shane Lowry and Adam Scott also failed to make the weekend.
Jon Rahm's US Open challenge came to a dramatic end on Friday as the Spaniard slumped to a second-round 78 and missed the cut after a six-shot collapse over a disastrous five-hole stretch.
Wyndham Clark surged four shots clear at the US Open after Thursday's rain-affected opening round, while Rory McIlroy began steadily and Scottie Scheffler has some work to do.
Rory McIlroy will begin his quest for a second major title of the year alongside Ryder Cup teammates Tommy Fleetwood and Ludvig Aberg.
Designed by William Flynn in 1894, Shinnecock Hills is one of the US Open’s most famed host venues – and is also feared for being among the toughest of all of them.
