Fernandez-Castano had nine birdies and three bogeys in shooting 6-under-par 72. He had a one-stroke lead over John Daly, who shot a bogey-free 67.
K.J. Choi and Jason Day each shot 4-under 68 and are tied for third with five other players turning in 3-under 69s.
Play was hampered by heavy winds, with desert sands limiting visibility.
Fernandez-Castano opened with a birdie at the Doha Golf Club but slipped back to even with a bogey at No. 4. He quickly answered with a birdie at the fifth hole and jumped to 3-under by closing the front nine with back-to-back birdies.
He went bogey-birdie at Nos. 10 and 11 before another bogey at 13. Fernandez-Castano closed in the flurry, however, getting a birdie at 14 and then three straight birdies at 16-18 for the lead.