The man reportedly fired two shots with a rifle at the female bear, who was wandering with her cubs at the time, killing the animal instantly.
Local media report that the man suffered serious leg injuries and was taken to a hospital in Toulouse.
Police are now investigating the Saturday afternoon incident.
The man, part of a local hunting association in the Seix region of Ariège, had been bitten by the bear several times, causing damage to the arteries in his legs, police said.
AFP news agency reports that a source close to the case said the man was in a serious condition.
Police said they responded to an emergency call at about 15:30 local time (14:30 GMT) and when they arrived at the scene, they discovered the dead bear just metres from where the hunter was lying injured.
A member of the same hunting association, who was not named, told local news website La Depeche that he heard a call for help on a radio the group uses while hunting, and made his way to the scene of the attack.
“One person managed to stop the bleeding until help arrived,” he said.
A local council official in Ariège, Christine Tequi, said that such attacks were “what we feared”.
“Today, you can really see that cohabitation is complicated,” she told AFP.
France began reintroducing brown bears to the Pyrenees after numbers of the animals plummeted in the 1990s.
But the move has sparked protests from local farmers who say the bears pose a risk to their livestock.