Badoer began kart racing in 1985, winning regional titles around Venice before becoming Italian national karting champion in 1987 and Italian champion in the 100cc international class in 1988. He moved to single-seater racing in 1989 in the Italian Formula Three Championship and developed steadily over three seasons, winning four consecutive races in 1991 before a technical disqualification over tyre regulations cost him a higher championship finish.
In 1992 Badoer graduated to the Formula 3000 Championship, driving for Crypton Engineering. He won four races — including a dominant display at Pergusa where he finished 21 seconds ahead of Emanuele Naspetti — and became one of only four drivers to win the Formula 3000 title at the first attempt, joining Stefano Modena, Christian Fittipaldi and later Jörg Müller in that exclusive group. His rivals that year included Rubens Barrichello and David Coulthard.
Badoer turned down a Tyrrell contract for his Formula One debut and instead signed with BMS Scuderia Italia, whose Lola chassis with Ferrari engines proved the slowest qualifier in the 1993 field. Despite this, Badoer demonstrated composure and occasional pace — his best result was seventh at Imola — and finished the season before the team merged with Minardi.
After a year as Minardi's test driver, Badoer took over Michele Alboreto's race seat at Minardi in 1995. The team operated on limited funds and with a Ford V8 after a hoped-for Mugen-Honda deal fell through. Badoer achieved eighth places in Canada and Hungary as his best results. In 1996 he moved to Forti Corse, qualifying for only six of ten races the team entered. A heavy collision with Pedro Diniz in Argentina — Diniz's Ligier struck Badoer from behind and flipped the Forti upside down — ended without injury to Badoer, though Argentine safety marshals drew criticism for their response. Forti Corse folded after the 1996 British Grand Prix.
Badoer was hired as Scuderia Ferrari's test driver in 1997, a role he would hold for twelve years. He spent thousands of kilometres each year at the Mugello and Fiorano test circuits and is credited with making a vital contribution to Ferrari's first Formula One Drivers' Championship win for 21 years in 2000. At the opening ceremony of the 2006 Winter Olympics in Turin, Badoer performed doughnuts in a Ferrari F1 car before an assembled crowd.
Badoer returned to racing in 1999 with Minardi. His most agonising moment came at the chaotic 1999 European Grand Prix at the Nürburgring, where he ran as high as fourth before gearbox failure ended his race thirteen laps from the finish. His teammate Marc Gené inherited that position and scored a point — widely regarded as a decisive factor in Ferrari's Eddie Irvine narrowing the gap to Mika Häkkinen in the Drivers' Championship. Badoer reportedly broke down in tears after the retirement. Earlier in the season, a testing accident had left him with a broken hand, costing him the Brazilian Grand Prix. When Michael Schumacher broke his leg at Silverstone in July, Badoer expected to be promoted to the Ferrari race seat as the team's test driver, but Mika Salo was chosen instead.
Badoer's only Formula One starts for Ferrari came in 2009 after Felipe Massa was struck on the helmet by debris from Rubens Barrichello's Brawn GP car during qualifying for the Hungarian Grand Prix, fracturing his skull. Michael Schumacher was lined up to replace Massa but a neck injury forced him to withdraw. Ferrari gave the seat to Badoer.
After nearly ten years away from racing — the second-longest gap between race entries in Formula One history — Badoer struggled at the 2009 European Grand Prix in Valencia. He qualified last and finished seventeenth out of eighteen finishers, though his fastest lap was quicker than both Toro Rosso drivers. At the Belgian Grand Prix he again qualified last, finishing fourteenth. Ferrari replaced him with Force India's Giancarlo Fisichella for the Italian Grand Prix onward. Badoer blamed negative media coverage for the decision.
Badoer retired from his Ferrari test driver role at the end of 2010, replaced by Jules Bianchi. His farewell demonstration in the Ferrari F60 took place at the Bologna Motor Show in December 2010, followed by a drive on ice at Madonna di Campiglio in January 2011. His son Brando entered karting in 2017 and competed in Italian Formula 4 with Van Amersfoort Racing, also being part of the McLaren Driver Development Programme until 2025.
Badoer's career is a study in talent defined by circumstance. The Formula 3000 title at the first attempt announced a significant talent; the years spent at Scuderia Italia, Minardi and Forti — among the least competitive cars in the field — denied him the results that talent deserved. His record of 50 starts without a point is an artifact of both the era's narrow points structure and his placement consistently at the back of the grid. As Ferrari's principal test driver through the team's most successful period, his contribution to the sport extended well beyond his race entries.