Gounon raced in French Formula Renault between 1985 and 1987, finishing as runner-up twice, before moving to French Formula Three. He placed fourth in the 1988 championship and won the title in 1989, driving for Oreca in a Reynard-Alfa Romeo and taking five victories during the campaign.
He stepped up to International Formula 3000 in 1990 with Madgwick Motorsport, driving a Reynard-Honda, and finished ninth in the championship. In 1991 he joined the 3001 International squad, switching to a Ralt-Cosworth, and won the round at Pau — one of the few victories that season not scored in Reynard machinery. That year's Enna round also involved a disputed jumped-start ruling against Gounon, made before electronic detection systems became standard, which cost him what would likely have been a further victory.
For 1992 he drove for DAMS in a Lola-Cosworth. He won the final round of the season at Magny-Cours and ended the year seventh in the standings. Across the 1991 and 1992 seasons, Gounon was the only F3000 driver to win in both Ralt and Lola machinery against Reynard-dominated grids.
Gounon's path into Formula One was complicated. For 1993 he was originally signed by March, but the constructor collapsed before the season began. He later arranged a two-race entry with Minardi after Christian Fittipaldi was dropped, contesting the Japanese and Australian Grands Prix; he completed neither race.
The 1994 season offered a more sustained opportunity. He raced briefly in French Supertouring at the wheel of a BMW 318is, where he recorded a sixth-place finish, before stepping in at Simtek mid-season after Andrea Montermini broke his leg. He qualified for all seven Grands Prix he entered. At the French Grand Prix at Magny-Cours — his home race — he finished ninth, a result that equalled Simtek's joint best-ever placing in Formula One. His F1 career ended after the Portuguese Grand Prix, when he was replaced by the better-funded Domenico Schiattarella.
Gounon made his 24 Hours of Le Mans debut in 1995 sharing a Venturi 600LM, which was not classified at the finish. In 1996 he competed in the BPR Global GT Series in a Ferrari F40 GTE, collecting three podium finishes and placing fifth in the championship standings.
The high point of his career came at the 1997 24 Hours of Le Mans. Sharing the McLaren F1 GTR numbered 41, entered by Gulf Team Davidoff, alongside Pierre-Henri Raphanel and Anders Olofsson, Gounon finished second overall and first in the GT1 class. The result placed the crew at the top of the GT1 order in one of the strongest McLaren-era fields the race had seen.
In 1998 Gounon drove for Persson Motorsport in the FIA GT Championship, piloting a Mercedes-AMG CLK GTR. He took a second-place finish at the Oschersleben round. The 1999 season saw the Mercedes CLK LM programme withdrawn from Le Mans following two catastrophic airborne accidents, bringing his association with the AMG effort to a close.
Through the 2000s he continued in endurance racing under various arrangements. He drove for DAMS and BMS Scuderia Italia, and also competed with Courage Competition. At the 2005 24 Hours of Le Mans he shared an Audi R8 and finished fourth overall. He accumulated eleven starts at Le Mans across his career.
Gounon participated in the 2017 Race of Legends, finishing sixth. His son Jules Gounon, born during the 1994 Formula One season in which Jean-Marc raced for Simtek, went on to establish a professional racing career in his own right.
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