Van Pelt went bogey-free on day one of the FedEx Cup play-offs opener, with an eagle and four birdies giving him the outright lead at the Ridgewood Country Club in Paramus, New Jersey.
The 39-year-old American - 104th in the FedEx Cup rankings - started the round with three successive birdies on the front nine before adding another at the 16th hole.
Van Pelt, who is without a PGA Tour win since claiming the 2009 US Bank Championship in Milwaukee, holed for an eagle at the 17th to be a shot clear of eight men tied for second.
Americans Cameron Tringale, Hunter Mahan, Charles Howell III, Ben Martin, Brendon Todd and Jim Furyk, Zimbabwean Brendon de Jonge and Englishman Paul Casey are all level at five under through the first 18 holes.
Van Pelt is nine strokes ahead of in-form world number one and FedEx Cup leader McIlroy, who fired a three-over-par 74.
McIlroy - aiming to add to his three consecutive triumphs at The Open Championship, WGC-Bridgestone Invitational and the US PGA Championship - had a double bogey and three bogeys throughout his poor first round.
The Northern Irishman did close the round with a highlight - a 32-foot birdie putt at his final hole on Thursday.
Japan's Ryo Ishikawa, Scotsman Russell Knox and New Zealander Danny Lee are tied at four under as they round out the top 10.
Dual Masters champion Bubba Watson - third in the rankings - headlines a group of 19 players tied for 13th spot.
Joining Watson at three under are Erik Compton, Steven Bowditch, Justin Hicks, Daniel Summerhays, Rickie Fowler, John Senden, Hideki Matsuyama, William McGirt, Kevin Chappell, K.J. Choi, Jason Bohn, Seung-Yul Noh, Justin Rose, Zach Johnson, Matt Kuchar, Keegan Bradley, Ernie Els and Ricky Barnes.
Defending champion and Australian world number two Adam Scott - 15th in the FedEx Cup rankings - is two-under overall alongside 12 others.
Meanwhile, last year's FedEx Cup champion Henrik Stenson of Sweden started with a one-over-par 72.