Mr Fox is an anthropomorphic, tricky, and clever fox who lives underground beside a tree with his wife and four children. To feed his family, he makes nightly visits to local farms owned by three cruel, rude, wicked and dim-witted farmers named Boggis, Bunce, and Bean, stealing poultry from each. Tired of being outsmarted by Mr Fox, the triumvirate devise a plan to ambush him as he leaves his burrow, but they succeed only in shooting off his tail.
The three farmers then dig up the Foxes' burrow using spades and then excavators. The Foxes manage to escape by burrowing further beneath the ground to safety. The farmers are ridiculed for their persistence, but they refuse to give up and vow not to return to their farms until they have caught Mr Fox. They then choose to lay siege to the Foxes, surrounding the hole and waiting until Mr Fox becomes hungry enough to come out. Cornered by their enemies, Mr Fox and his family, and all the other underground creatures that live around the hill, begin to starve.
After three days trapped underground, Mr Fox devises a plot to acquire food. Working from his memory of the aboveground routes he has used, he and his children tunnel into Boggis's four chicken houses. Mr Fox kills several chickens and sends his son to carry the animals 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, as well as to extend an invitation to the feast to the other burrowing animals - Badger and his family, as well as the Moles, the Rabbits and the Weasels - to apologize for getting them caught up in the farmers' hunt. Aided by Badger, the animals tunnel to Bunce's storehouse for additional food, and then to Bean's secret cider cellar. Here, they are nearly caught by Bean's servant Mabel and have an unpleasant confrontation with the cellar's resident, Rat. 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 on their behalf daily and where none of them will need to worry about the farmers anymore. Everyone joyfully cheers for this idea, while Boggis, Bunce, and Bean are left waiting in vain for Mr Fox to emerge from his hole.
The book ends with the words "And so far as I know, they are still waiting".
