Lydia Ko, who recently lost her world number one crown, is six shots back. Her successor, Thailand's Ariya Jutanugarn, is eight off the pace.
Henderson made four straight birdies from the ninth hole and looked like having a handy halfway lead until dropping shots at her final two holes.
A three-times winner on the LPGA Tour, Henderson has recorded just one top-five finish this season.
“It's been a little bit of a rough season so far, not getting the results that I've been looking for but this week seems to be a turnaround week and hopefully I can just finish strong the next two days,” Henderson told reporters.
“Two bogeys to finish, but that just gives me a little more motivation going into tomorrow.”
Ciganda, meanwhile, surged into contention with an eagle and five birdies on the same course where she lost a playoff to Kim Sei-young last year.
“Obviously I saw (Henderson) playing good, and when she’s on, it’s hard to beat her but I’m excited to keep fighting,” said Ciganda, a two-time LPGA winner.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Peter Rutherford)
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