Kathryn Marshall, Emilee Klein, Heather Bowie, Beth Daniel, Alison Nicholas and Silvia Cavalleri are a shot behind at 5-under while Juli Inkster, Sherri Steinhauer, Vicki Goetze-Ackerman and Leta Lindley are at minus-four.
Pepper started on the second nine at Eagles Landing Country Club and carded her first birdie at the 14th hole when she drilled a five-footer. She added two more at the turn when she holed a four-footer at No. 17 and then got up and down from a bunker at the par-5 18th.
Pepper chipped in for eagle from 35 feet with a sand wedge at the sixth to get to 6-under.
'It's always an advantage in a 54-hole event to get out early before the greens are all tracked up,' said Pepper, who finished fourth last week in Texas. 'Today they were even better on the first nine than the back nine and were more receptive.'
Sanders mixed nine birdies and three bogeys on Thursday. Like Pepper, she opened on the back nine and got into red figures for the first time with a five-foot birdie putt at 13. She added another birdie with a 12-footer at 14 and then dropped her first shot at No. 15 when she two-putted from 15 feet.
She got back on track with five-foot birdie at the next hole when she nailed an 8-iron from the tee at the 188-yard hole. Sanders added another at the par-5 18th when she two-putted from 25 feet.
Sanders' second nine did not start well as she landed in a divot off the tee and never recovered, sailing her second shot over the green. Like the bogey at No. 16, Sanders answered with a six-foot birdie at the next hole. She scored back-to-back birdies at Nos. 4 and 5 with a pair of 15-footers.
The par-5 6th cost Sanders as she went out of bounds off the tee and failed to save par. She closed out with birdies at Nos. 7 and 8 to get to the top of the leaderboard.
'You had to be able to keep it on the green and the only way to do that was to be in the fairway and stop the ball okay on the greens,' said Sanders, who has never won on the LPGA Tour. 'That was what you have to do from the first hole to the last hole.'
Defending champion Sophie Gustafson is part of a group of golfers tied for 22nd at minus-two. Tournament host Nancy Lopez is in that group as is Annika Sorenstam, who won four starts in a row earlier this season.
Full-field scores from the Chick-fil-A Charity Championship