MEMPHIS, 13 Jun 2015 (AFP) - Koepka fired a three-under-par 67 at TPC Southwind in Memphis for a nine-under total of 131.
He had a one-stroke lead over fellow American Austin Cook, who surged up the leaderboard with a six-under 64.
New Zealand's Steven Alker led during the round, but faded late, finishing with a bogey at the par-three eighth followed by a double-bogey at the ninth in a 68 for 133.
"I let it slip at the end," said Alker, who had moved as low as 10-under. "That's the type of golf course it is."
Alker was still pleased to find himself in Saturday's final group as he searches for a first top-25 finish this season.
"It's fun," he said. "I haven't been in this position all year. A bad finish, but a lot of positives."
England's Greg Owen, who shared the overnight lead with Koepka and Ryan Palmer, signed for a 70 to join a group of seven players sharing fourth place on 134.
Palmer posted a one-over 71 to fall into a tie for 11th.
Koepka saw his form drop off after a solid start to the season that included a victory in the Phoenix Open.
He added this week's tournament at the last minute in a bid to sharpen his game for the US Open, and said he was managing to stick to his game plan of playing less aggressive, more patient golf.
"I'm just playing really solid," Koepka said. "Not really too exciting, just playing solid golf -- no mistakes."
Five-time major champion Phil Mickelson, also tuning up for a US Open tilt next week at Chambers Bay, posted a one-under 69 that left him three-under and six shots off Koepka's lead.
Mickelson saw a few birdie chances just fail to fall, but said he couldn't call the greens unfair.
"They don’t owe me anything," he said. "They're trickier because they're fast."
Mickelson remained optimistic about his weekend chances since he "hit a lot more good shots" to reach the greens.
"There aren't holes that are just 'gimme' birdies that can kind of kick-start your round," he said. "But if I can shoot five-, six-, seven-under par, I'll be right in contention on Sunday."
Leading second-round scores on Friday in the US PGA Tour St. Jude Classic (USA unless noted, par-70):
131 - Brooks Koepka 64-67
132 - Austin Cook 68-64
133 - Steven Alker (NZL) 65-68
134 - Chris Smith 67-67, Russell Knox (SCO) 70-64, Fabian Gomez (ARG) 66-68, Scott Brown 65-69, Tom Gillis 66-68, Greg Owen (ENG) 64-70, Tom Hoge 69-65
135 - Kevin Chappell 71-64, Ryan Palmer 64-71, Chad Campbell 69-66, Spencer Levin 67-68
136 - Harris English 69-67, David Toms 70-66, Matt Jones (AUS) 69-67, Colt Knost 72-64, Jason Gore 71-65, Mark Wilson 67-69, Ben Crane 66-70
137 - Chad Collins 71-66, Brian Davis (ENG) 65-72, Arjun Atwal (IND) 72-65, Boo Weekley 67-70, Phil Mickelson 68-69, John Merrick 69-68, Luke Donald (ENG) 69-68, John Rollins 67-70