Naamen Meziche, 33, who had been in Pakistani custody for more than a year, was charged after arriving in France with participation in a conspiracy to commit terrorism.
Radio France Internationale said Saturday French intelligence officials had Meziche on their radar for 10 years. He was suspected of being a member of al-Qaida's so-called Hamburg cell, which included a number of Sept. 11, 2001 terrorists in its ranks.
Meziche, a French citizen of Algerian descent, was picked up in rural Pakistan last year along with three other French citizens. French intelligence agents planned to interrogate him in connection with a case opened in March, RFI said.
A source told the BBC the new case was based on information from German authorities dating back to 1990.
Meziche lived in Germany for several years and allegedly recruited jihadists at a Hamburg mosque that was shut down in 2010.