Gené began in karting, finishing runner-up in the 1987 Catalan Kart Championship and winning it outright in 1988 along with the Spanish National Class Kart Championship. He competed in the European and World kart championships in 1989, and in 1990 became the youngest driver to win the Senior Class of the Spanish Kart Championship.
He moved into single-seaters in 1992 with Formula Ford, placing fifth in the Spanish championship. In 1993 he was runner-up in the European Championship and took second at the Formula Ford World Cup and Festival. His British Formula 3 debut in 1994 earned him Rookie of the Year honours; he placed tenth in the championship in 1995. In 1996 he won the FISA Superformula championship, followed by a six-round FIA Formula 3000 campaign in 1997, and in 1998 he clinched the Open Fortuna by Nissan Championship with six wins and three pole positions.
Gené's Formula One career began in 1999 with the Minardi team. Despite the team's limited resources, he delivered a breakthrough result at the 1999 European Grand Prix at Nürburgring — a sixth-place finish that scored Minardi's first point since 1995. The race was notable for the misfortune of his teammate Luca Badoer, whose gearbox failed with 13 laps to go while running fourth, denying Badoer his first career points.
In 2000, Gené remained with Minardi alongside Gastón Mazzacane but failed to score any points, his best results being eighth-place finishes in Australia and Austria. Over two seasons he accumulated 36 Formula One starts and five career points.
Unable to secure a competitive race drive for 2001, Gené became a test driver for Williams, a role that occasionally led to race appearances as a substitute. He stepped in for the injured Ralf Schumacher at the 2003 Italian Grand Prix, finishing fifth to score four points. Following another Schumacher back injury at the 2004 United States Grand Prix, Gené drove for Williams at the French and British Grands Prix before losing the seat to Antônio Pizzonia.
In November 2004, Gené signed with Scuderia Ferrari as a test driver alongside former Minardi teammate Luca Badoer. His contract was renewed for 2007, though increasing restrictions on testing limited his on-track time. At the end of 2010 he was replaced by Jules Bianchi ahead of the 2011 season.
Peugeot recruited Gené as a factory driver for their 908 HDi FAP programme in the Le Mans Series and at the 24 Hours of Le Mans from 2007 onwards. A serious crash in practice for the 2008 24 Hours of Le Mans left him with a broken toe, but the following year went very differently. In 2009, sharing a Peugeot 908 with David Brabham and Alex Wurz, Gené completed 382 laps to win the 24 Hours of Le Mans outright — ending a run of recent Audi dominance and delivering the win to a French-manufactured car. Gené drove the final stint and brought the car home to a standing ovation from the crowd.
He also competed in the 1000 km Spa in both 2008 and 2009, winning in 2008.
From the 2010 season, Gené transitioned into television commentary, covering Formula One for Spanish broadcaster Antena 3. In 2013 he joined Sky Sport F1 HD in Italy as an expert analyst, a role he has maintained alongside his ongoing position as Ferrari brand ambassador.
Grands Prix started: 36 — Points: 5 — Best championship position: 17th (2003) — Best race classification: 5th (2003 Italian Grand Prix)