Gibernau began competitive motorsport in observed trials before switching to road racing in 1990 and winning the Spanish Juniores 125cc Championship in 1991. He made his Grand Prix debut as a wildcard at the 1992 Spanish Grand Prix on a Yamaha entered by Wayne Rainey's team, and contested occasional wildcard rounds through 1995. His first full season came in 1996 in the 250cc World Championship with the Axo Honda team, where he scored 20 points in 22nd place.
Moving to the 500cc World Championship in 1997 with Team Rainey's Yamaha, Gibernau recorded a best finish of sixth in Australia and placed 13th overall. He joined Honda as a privateer in 1998, taking a podium at Madrid. In 1999 he stepped into the factory Honda NSR500 vacated by injured five-time champion Mick Doohan, finished second at the South African round behind Max Biaggi, and ended the season fifth with 165 points. After a crash-disrupted 2000, he moved to Suzuki and claimed his maiden class victory at the rain-shortened 2001 Valencian Community round by switching to slick tyres before rivals, finishing ninth in the championship.
Gibernau's transfer to Honda's Gresini Racing team for 2003 proved transformative. Following teammate Daijiro Kato's fatal accident at the season opener, he was given a full works-specification machine and won four races — South Africa, France, the Netherlands and Germany — the German victory by just 0.060 seconds. He finished second in the championship with 277 points, 80 behind Valentino Rossi.
In 2004, with Rossi having switched to Yamaha, Gibernau won four more races and mounted a sustained title challenge, but a controversial qualifying incident at the Qatar round — in which Rossi's team tampered with his grid position — heightened rivalry between them, and he again finished runner-up with 257 points. A troubled 2005 brought five pole positions but no race victories; a particularly aggressive pass by Rossi on the final corner of the Spanish Grand Prix ignited further controversy. He finished seventh with 150 points.
Joining factory Ducati in 2006, Gibernau suffered a catastrophic first-lap crash at Catalunya when teammate Loris Capirossi's brake lever caused his machine to cartwheel, leaving him with a concussion, a fractured hand, and a broken collarbone. He retired at the end of the season, having scored 95 points in 13th place.
Gibernau made a brief comeback in 2009, scoring 12 points across six starts. He subsequently competed in the electric MotoE World Cup in 2019, riding an Energica motorcycle to 11th overall with 38 points across six races.
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