SAN MARTIN, October 13, 2013 (AFP) - The 23-year-old, who has European Tour status after winning three times this year on Europe's Challenge Tour developmental circuit, had six birdies and two bogeys to build a 54-hole total of 15-under 198, two strokes in front of George McNeill and Jason Kokrak.
Kokrak carded a 68 while McNeill climbed the leaderboard with a course-record equaling nine-under par 62 for 200.
Jimmy Walker also notched a 62 at CordeValle Golf Club, and was in a group on 201 alongside former world number one and three-time major champion Vijay Singh of Fiji and American Robert Garrigus.
Singh posted a 65, while Garrigus carded a 68.
While Koepka's success on the Challenge Tour has earned his playing privileges on the European Tour, the Floridian could earn US PGA Tour status with a win on Sunday.
The $5 million tournament, formerly part of the season-ending "Fall Finish," is this year the first event in the US Tour's new-style 2013-2014 season, with FedEx Cup playoff points on offer and a Masters berth for the winner.
"I've just got to approach it the same way," Koepka told the Golf Channel of his strategy for Sunday. "We've got a good game plan and things seem to be going pretty well. I just have to stick to it and everything will take care of itself."
Kokrak birdied his last two holes on Saturday to get into the final group on Sunday.
His round was highlighted by an eagle at the par-four first, where he holed out from 130 yards.
Kokrak, who is also chasing his first US PGA Tour title, was runner-up here last year to Sweden's Jonas Blixt.
McNeill had 10 birdies and one bogey in his 62.
"It was a lot of fun," he said. "Sixty-two, I don't know how it could ever not be fun."
Walker also had 10 birdies and a lone bogey as he tied the course record he set himself in the final round last year.
Leading third-round scores on Saturday in the $5 million US PGA Tour Frys.com Open (USA unless noted):
198 - Brooks Koepka 67-64-67
200 - George McNeill 68-70-62, Jason Kokrak 67-65-68
201 - Jimmy Walker 70-69-62, Vijay Singh (FIJ) 69-67-65, Robert Garrigus 70-63-68
203 - Will MacKenzie 69-70-64, Max Homa 69-68-66, Ben Martin 69-68-66, Ryo Ishikawa (JPN) 69-67-67, Jim Herman 67-66-70
204 - Ricky Barnes 71-69-64, Kevin Chappell 70-69-65, Briny Baird 71-68-65, Justin Hicks 68-68-68, Billy Hurley 69-66-69, Hideki Matsuyama (JPN) 70-66-68, Spencer Levin 71-65-68, Charlie Wi (KOR) 67-68-69
205 - Brian Davis (ENG) 70-69-66, Jeff Overton 64-72-69, Andres Gonzales 74-62-69
206 - Brian Harman 65-74-67, John Peterson 68-70-68, James Driscoll 74-67-65, Sean O'Hair 71-70-65, J.J. Henry 67-71-68, Kevin Na 75-67-64, Scott Brown 68-67-71