Fernandez fired a 5-under-par 67 at The National Golf Club of Kansas City to soar past faltering first-round leader Jose Maria Canizares of Spain.
One day after steady rain made conditions tricky and helped contribute to just six scores under par, Fernandez signed for one of three 67s and climbed to 6-under 138. Mike McCullough and Ireland's Des Smyth bounced back from opening-round 73s and are tied for second at 140 with former Player of the Year Allen Doyle and Jay Sigel.
It is another shot back to James Mason and Butch Sheehan, with Hale Irwin among four players at 2-under 142. One is Pat McDonald, a Champions Tour rookie who collected nine birdies en route to a 7-under 65 - the best score of the weekend.
Fernandez had four bogeys on the front nine and never got untracked, carding a 3-over 75 to fall six shots back.