After becoming the first driver to win 4 races in his rookie IndyLights season, he moved up to IndyCar for 1993. He took his first victory in the championship in 1996 at Toronto, but was not a regular front-runner until he joined Patrick Racing in 1998. He took two victories and 4th overall that year, and two more wins en route to 6th in 1999. In 2000 he came close to winning the championship, despite not starting on the front row all season - he scored points in 17 of the 20 races including 2 wins and 3 further podium results.

In 2001 he founded Fernandez Racing, with former Ganassi manager Tom Anderson as his partner, and ex-F1 driver Shinji Nakano as his team-mate. He finished 3rd twice and took 2 poles that year, but his team's first victory came at Portland in 2003, the first win for an owner-driver since Bobby Rahal achieved the feat in 1993. That year he also ran an IRL entry for Asian-American Roger Yasukawa, in partnership with Aguri Suzuki, and for 2004 he moved the whole team to the series. Despite taking 3 wins and 4th overall in the 2004 IRL, he was unable to secure funding to race in 2005 - Delphi are Sharp's personal sponsor while engine suppliers Honda insisted on Japanese driver Matsuura.

In 2005 he drove the 5 Lowe's / Hitachi Chevrolet in Mexico for Rick Hendrick in the fistNASCAR Busch Series race held outside the United States. In this race, (called the Telcel Motorola 200) Fernandez raced in a one time ride to help promote NASCAR racing to the local fans. He led several laps in the race before giving up the lead to eventual race winner Martin Truex Jr.. It was announced that he would run 4 more races in the Busch Series for Hendrick Motorsports.

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