Born into a racing family — his father Patrick raced in touring cars and sports cars — Bourdais began karting aged ten. He won the Maine Bretagne League in 1991 and the Cadet France karting championship in 1993. Moving into formula cars in 1995 via Formula Campus by Renault, he progressed through French Formula Renault (runner-up in 1997 after four wins), won the French F3 series in 1999 with eight wins, and graduated to International F3000, where he drove for the Prost Junior Team before moving to DAMS and Super Nova Racing. He won the F3000 championship in 2002, beating Giorgio Pantano by two points after the disqualification of Tomáš Enge.
Bourdais joined Newman/Haas Racing for the 2003 CART season. In his very first race at St. Petersburg, Florida, he became the first rookie since Nigel Mansell to take pole position on debut. He won at Brands Hatch in his fourth race, claimed five more podiums, and finished fourth in the championship to win the Rookie of the Year award.
He then dominated Champ Car over four consecutive seasons. In 2004, seven wins and eight poles in his McDonald's-sponsored Lola secured the title by 28 points over team-mate Bruno Junqueira. The 2005 title followed on the strength of five wins in the final six races. In 2006 he won a third consecutive championship, becoming the first Champ Car driver to achieve three consecutive titles since Ted Horn in 1948. A fourth title came in 2007 with victory at the Lexmark Indy 300.
After four Champ Car championships, Bourdais was confirmed as a Scuderia Toro Rosso driver from 2008, partnering Sebastian Vettel. His first race, the 2008 Australian Grand Prix, saw him ultimately classified eighth. He scored his best result of the season at the Belgian Grand Prix, finishing seventh after running as high as third. At Monza, despite having to start from the pit lane after a gearbox issue on the grid, he set the second-fastest lap of the race.
A second year with Toro Rosso began for 2009 alongside rookie Sébastien Buemi, but Bourdais struggled to match his team-mate's pace. After a series of incidents and poor form, Toro Rosso announced his departure on 16 July 2009. The team subsequently settled out of court for $2.1 million following breach of contract proceedings. Bourdais started 27 Formula One races in total.
Bourdais first contested the 24 Hours of Le Mans in 1999 aged twenty, sharing a Porsche 911 GT2 with Pierre de Thoisy and Jean-Pierre Jarier for Larbre Compétition before retiring with engine failure.
His most sustained endurance programme came as a Peugeot Sport factory driver from 2007 to 2011. In 2007 he co-drove a factory Peugeot 908 HDi FAP with Stéphane Sarrazin and Pedro Lamy to second place, and in 2009 again finished second in the Peugeot. The 2010 race ended before Bourdais could take the wheel after a co-driver's suspension failure.
In 2016, as a Ford Performance factory driver, Bourdais won the GTE-Pro class at the 24 Hours of Le Mans — the race of his hometown — completing a career arc that took him from spectator to factory winner at the circuit bearing his city's name.
Bourdais rejoined American open-wheel competition in 2011 following his Formula One career, running with Dale Coyne Racing. After stints at Dragon Racing (2012–13) and KV Racing, he joined Dale Coyne Racing again for 2017 and won the Firestone Grand Prix of St. Petersburg on the opening weekend after starting from last due to a qualifying crash. On 20 May 2017, a single-car accident during Indianapolis 500 qualifying resulted in multiple pelvic fractures and a fractured right hip; he returned later in the season and was back to full form in 2018, winning the St. Petersburg opener again. Bourdais announced after the 2021 season finale at Long Beach that he would step back from full-time IndyCar competition to focus on sportscar racing.
Alongside open-wheel competition, Bourdais accumulated significant sportscar results. He won the Spa 24 Hours in 2002, the Rolex 24 at Daytona in 2014 with Action Express Racing in the Corvette DP alongside João Barbosa and Christian Fittipaldi, and the 12 Hours of Sebring in 2015 with the same team. In July 2012 he won the inaugural Brickyard Grand Prix Rolex Sports Car Series race at Indianapolis Motor Speedway.
From 2022 he focused predominantly on sportscar duties, first with Chip Ganassi Racing in IMSA and then signing with Cadillac Hertz Team Jota for WEC Hypercar competition in 2024.
Bourdais won the Gold Coast 600 V8 Supercar race in 2011 and again in 2012 alongside Jamie Whincup, receiving the inaugural Dan Wheldon Memorial Trophy on both occasions. He was the first driver to win at the Surfers Paradise Street Circuit in both Champ Car and V8 Supercar competition.
With four consecutive Champ Car titles, 37 American open-wheel victories (76 career wins in total as of early 2025), a Le Mans GTE-Pro class win, and multiple IMSA and endurance victories, Bourdais stands as one of the most versatile and enduring professional racing drivers of his era. His Champ Car record places him alongside the sport's all-time greats, and his ability to compete at a high level across open-wheel, GT, and prototype categories over more than two decades sets him apart in modern motorsport.