Karlsson, who lost in a playoff to Lee Westwood at this event a year ago, shot a 5-under 65 at the TPC-Southwind course. That was one of three such scores produced Friday and gave him a 36-hole total of 131.
He has won 11 times on the European Tour, including last year's season-closing event in Dubai, but he is still looking for his first victory in the United States. This is the first time he has held the 36-hole lead at a tour event.
Colt Knost and recent Byron Nelson Classic winner Keegan Bradley shared second at 134 while John Merrick was alone in fourth at 135.
First-round leader David Mathis settled for a 72 that left him in a tie for seventh at 137. Westwood, the second-ranked player in the world, finished 36 holes at 139.
It took a score of 2-over 142 to survive the cut and John Daly was among those who made it. It was only the third time in 10 tournaments this year he has made the cut.
Those who missed out included David Toms and Sergio Garcia, who needed 11 shots to play the par-5 third hole during the opening round and eventually completed 36 holes at 147.