The 42-year-old Australian, chasing his 15th career PGA victory, stood on eight-under 134 after 36 holes at Wilmington (Delaware) Country Club.
“I’m playing well,” Scott said. “I’m in great shape going into the weekend. I don’t even know when the last time I led a tournament was.”
World number one Scottie Scheffler, the reigning Masters champion, and fellow Americans Cameron Young and Jordan Spieth shared second on 135 with Canada’s Corey Conners.
Four-time major winner Rory McIlroy chipped in for birdie from 31 feet at the 18th to shoot 68 and stand on 136 with American Scott Stallings and Aussie Cam Davis, defending FedEx Cup champion Patrick Cantlay and Tokyo Olympic champion Xander Schauffele.
The event is the second of three FedEx Cup playoff tournaments with the top 30 on season points after Sunday advancing to next week’s season-ending Tour Championship in Atlanta.
Scott, who has qualified for all 16 editions of the playoffs, is set to jump into to third in points from 45th and reach Atlanta for the first time since 2019.
“As much as I want to make it to the Tour Championship I’d love to win the BMW Championship first,” he said.
The Aussie sank a birdie putt at the opening hole from just inside nine feet and added 22-foot birdie putts at the fourth and sixth holes.
Scott, whose most recent PGA triumph came in 2020 at Riviera, added a birdie putt from just outside five feet at the par-5 12th but his tee shot at 17 landed behind a tree. He blasted into nearby rough then missed the green on his way to a double bogey.
“A poor shot on 17 was quite costly,” Scott said. “It’s a good reminder for the weekend that I’ve really got to keep it under control.
“But I kept it in position really well all day, had so many good looks and was cruising there for a while.”
Spieth matched Scott with an 18-foot biride putt at the 17th before missing the 18th green and closing with his lone bogey to shoot 67.
“Managed my way around the golf course really well,” Spieth said. “Two bogeys for the two rounds allows me to settle in and not feel like I have to force anything.”
Scheffler opened with three birdies, all on putts inside five feet, on his way to a 67.
“I got off to a really good start. After that it was pretty mediocre,” Scheffler said. “Overall, I’m pleased with the round.”
Young had seven birdies and four bogeys to shoot 68.
“It was a little bit messy,” Young said. “There was a lot of potential to shoot something a lot lower, but just was a little bit clumsy around the greens.”
Conners answered his lone bogey at 16 with a closing nine-foot birdie putt to shoot 67.
“I’m striking the ball well,” said Conners. “Feel good about the game going into the weekend.”
McIlroy’s revenge at 15
McIlroy dropped his tee shot within four feet of the cup to set up a birdie at the par-3 15th, the same hole where he suffered a nightmare triple bogey on Thursday.
“Coming off the golf course a lot happier than I was last night. Really happy with how I played. I bounced back well,” McIlroy said.
“That was nice to make two there (at 15). The chip in on the last was really nice too.”
American Keegan Bradley, the 18-hole leader and 2018 BMW winner, fired a 74 to stand on 138.
Cup points leader Will Zalatoris, this year’s PGA Championship and US Open runner-up, was on 139 after a 69.