It took several hours to remove the unwanted passenger from the flight bound for the French capital in the early hours of Saturday.
By the time the stowaway had been expelled, the cabin crew had reached the maximum time they are permitted to work to avoid fatigue, airline spokesman Christophe Paumier told AFP.
The flight was delayed by 48 hours and is expected to operate later Sunday.
Mice and other rodents are a significant danger to aircraft as they have a tendency to nibble through vital cabling.
“Air France regrets the inconvenience caused by this significant delay and recalls that the safety of its passengers and its crew is its top priority,” the airline said in a statement.