After Rory McIlroy destroyed the layout in the 2011 US Open, winning at a record 16-under, grounds staff ensured there would be no such blowout this year, with Van Pelt's four-under 67 one of just 22 rounds under par.
Tiger Woods was one of the many above par, as his short game struggled around the greens, and particularly in the sand. He posted a one-over 72 to be five off the pace in a tie for 30th.
Former world number one Vijay Singh of Fiji, American Jimmy Walker and Zimbabwe's Brendan de Jonge share second following rounds of 68.
Americans Billy Hurley III and Pat Perez, and Australia's Jason Day are tied fifth a shot further back.
Woods, the tournament host, confirmed he had nothing to do with the course set-up, but did believe there was some revenge in mind in its preparation.
"It's certainly, I think, a little retribution for what happened last year," said the 14-times Major champion, who missed last year's US Open with a knee injury. "But don't be mad at me, I didn't play.
"It was a pretty good grind out there. Not a lot of low scores on this golf course, especially this afternoon. It was baked out, the ball was springy, and it's hard to believe that four-under par is leading."
Woods expects conditions to toughen further as the course continues to dry out in the heat over the course of the week.
"I think it's going to be interesting as the week goes on, as it gets hotter, how this golf course is going to play because it's going to get baked out, and I don't think they're going to be able to put water on it while we're playing," he said.
"It'll be interesting to see how the afternoon guys do over the next three days."
Woods's hopes of finishing under par were undone by some poor shots from the sand late in his round.
"There's so much sand in these bunkers and my 60 is not built for this much sand," he said. "It's designed for less sand, so I have to make an adjustment and make sure I hit a little bit closer to the golf ball, and I just didn't do it."
Van Pelt was the only player to shoot a bogey-free round, with his total highlighted by an eagle on the first, his 10th, from 93 yards.
Day, runner-up to McIlroy in the 2011 US Open, enjoyed a return to form with his 69, but may have to rush off the course early with his wife Ellie expected to go into labour with their first child.
Day has already said he has a plane on stand-by.