The story revolves around an anthropomorphic, tricky, clever fox named Mr. Fox who lives underground beside a tree with his wife and four children. In order to feed his family, he makes nightly visits to farms owned by three wicked, cruel and dim-witted farmers named Boggis, Bunce, and Bean and snatches the livestock available on each man's farm. Tired of being outsmarted by Mr. Fox, the evil farmers devise a plan to ambush him as he leaves his hole, but they succeed only in shooting off his tail.
The farmers then dig up the Foxes' burrow using spades and then excavators. The Foxes manage to escape by burrowing further beneath the earth to safety. The trio of farmers are ridiculed for their persistence, so they decide to surround Mr. Fox's hole and wait until he is hungry enough to come out. Cornered by their enemies, Mr. Fox and his family, and all the other underground creatures, begin to starve.
Suddenly, Mr. Fox devises a plot to acquire food. He and his children tunnel through the ground and wind up burrowing to one of Boggis' henhouses. Mr. Fox kills several chickens and sends his eldest son to carry the food back home to Mrs. Fox. On the way to their next destination, Mr. Fox runs into his friend Badger and asks him to accompany him on his mission. Aided by Badger, the animals tunnel to Bunce's farm for ducks, geese, hams, bacon and vegetables, and then to Bean's cider cellar. Here, they are nearly caught by the Beans' servant Mabel, but have a narrow escape. They carry their loot back home, where Mrs. Fox has prepared a great celebratory banquet for the starving underground animals and their families. At the table, Mr. Fox invites everyone to live in a secret underground neighbourhood with him and his family, where he will hunt for them daily and none of them will any longer need to worry about the farmers. Everyone joyfully cheers for this idea, while Boggis, Bunce, and Bean are left waiting for the fox to emerge from his hole. The author concludes "And so far as I know, they are still waiting."