His talent apparent, Fernández made the jump to the CART IndyCar World Series in 1993, competing in five races for Galles Racing International. He ran his first full CART season in 1994 with Galles finishing 13th and capturing the "Marco Magaña" and "Luchador Olmeca" awards and the "JAC" trophy for "Best Driver" outside Mexico. Competing again with Galles in 1995, Fernández finished 12th in the standings placing in the top ten nine times.
Fernández moved to Tasman Motorsports in 1996. He had six top ten finishes, including his first career CART victory at Toronto. Unfortunately his delight at taking his first win was dampened by the fatal accident suffered by Jeff Krosnoff late in the race. The win in Toronto made him the first Mexican to win a CART event since Héctor Rebaque in 1982, and Fernández went on to finish 12th in the season points tally. However, 1997 was a disappointing season for Fernández. The Tasman team ran a Lola chassis which failed to perform to expectations. Through force of will, determination and talent, Fernández battled to three top ten finishes and 18th place in the PPG Cup standings.