Chapuis, born 21 March 1979 in Lyon, began his professional career at Niort in Ligue 2 before moving to Ligue 1 for Rennes in 2000. He was called up to the French Under-21s in 2000 and was part of the squad that lost to the Czech Republic in the final of the 2002 UEFA European Under-21 Football Championship.

After 13 goals in 44 appearances for Rennes, Chapuis signed a five-year contract for Olympique de Marseille in January 2002.

He joined Leeds on a season-long loan on 1 September 2003 after falling out of favour at the Stade Velodrome. Reid, who saw off Lens in negotiations for the striker, said at the time, 'His hold-up play is excellent, he can see people running, and he is strong. He is another one we've been able to get because of the change of coach at Marseille. It gives Michael Bridges that extra time to get fully fit and me another option up front which I didn't have.'

Chapuis was seen by many as a top striker and an absolute steal for Leeds, but he quickly disappeared into the reserves making only one league appearance against Bolton in November.

Chapuis played against Swindon and Manchester United in the League Cup and then he scored a second-half hat-trick in a testimonial match for Cambridge striker John Taylor on 11 November, with Leeds winning 5-3. That earned Chapuis a place on the bench for the Premier League match with Bolton at Elland Road on 22 November. He came on as a half-time substitute for David Batty.

In a move to cut costs, Leeds sent Chapuis back to Marseille in January 2004. He had further loan stays at Strasbourg and Ajaccio before being released in summer 2005, though he had been contracted them until June 2006. After trials with Rangers, he spent the latter part of 2005/06 with Belgian club FC Brussels. He joined Grenoble of Ligue 2 on 18 July 2006 on a free transfer. He joined FC Metz on an 18-month contract on 4 January 2008. However, he was no more than a bit part player as the club failed to avoid relegation.

Chapuis spent three years out of the game after being released by Metz in the summer of 2009. In 2012, he made a return with non-league Bourg-Péronnas. He helped them secure promotion back to Ligue 2 before he hung up his boots in 2014.