The Spaniard began the round tied for fifth place, five shots back, but moved to the top with a 13-foot birdie putt on the 15th hole while overnight leader Retief Goosen of South Africa made a bogey.
Fernandez-Castano parred his last three holes and with his 14-under 199, 54-hole total leads Goosen (69) and Germany's Martin Kaymer (66) by one shot heading into the final round at the historic Loch Lomond Golf Club.
"It's funny. On the range I couldn't hit a shot," he told reporters.
"Unfortunately my putting was not as good, but after a 64 I am not going to complain."
"One shot off the lead going into the final round is not a bad place to be," Goosen said.
Jamie Donaldson (65) of Wales and Denmark's Soren Kjeldsen (67) both are 11-under 202 to share fourth place.
Copyright 2009 by United Press International.