He frequented the top ten all session but with 2mins to run he banged in a super fast lap at his home track to nick provisional pole from SSP Yamaha rider Broc Parkes.
Parkes had jumped into first place with 3mins to run and looked like he would hold it until the former World Supersport Champ had other ideas.
Reigning World Supersport Champion Kenan Sofuoglu had to settle for third place although he did lead for most of the session. He wants to pick up his eighth race win of the year to beat Karl Muggeridge's record of seven wins in a season.
Gianluca Vizziello and Massimo Roccoli were running in fourth and fifth places respectively ahead of Katsuaki Fuijiwara who is recovering from a broken foot.
Spanish rider and last time out podium finisher, Joan Lascorz was running in seventh place on the Glaner Motocard.com Honda. David Checa on the GMT 94 Yamaha picked up eighth place just ahead of British rider Tommy Hill on the SSP Yamaha.
Gregory Leblanc completed the top ten on the Vazy Racing Honda. Craig Jones on the Reve Ekerold Honda was out side the top ten circulating in 13th place. The team are working on set-up for their machine at the tough French track as they have very little data available.
WSS qualifying results (1) – Magny-Cours:1. Sebastien Charpentier
2. Broc Parkes
3. Kenan Sofuoglu
4. Gianluca Vizziello
5. Massimo Roccoli
6. Katsuaki Fujiwara
7. Joan Lascorz
8. David Checa
9. Tommy Hill
10. Gregory Leblanc