The story revolves around an anthropomorphic, tricky, and 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 night visits to farms owned by three wicked, rude, cruel and dim-witted farmers named Boggis, Bunce and Bean and snatches away the livestock available on each man's farm. Although Mrs.Fox warns Mr.Fox that he should stop stealing, Mr.Fox continues to steal the livestock. Tired of being outsmarted by Mr. Fox, the farmers devise a plan to ambush him as he leaves his burrow, 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 that lived around the hill, begin to starve.
After three days trapped underground, Mr. Fox devises a plot to acquire food. Working from Mr. Fox's memory of the routes he has taken above ground, he and his children tunnel through the ground and wind up burrowing to one of Boggis' four chicken houses. 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, 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 them being caught up in the farmers' hunt because of him. Aided by Badger, the animals tunnel to Bunce's mighty storehouse for ducks, geese, hams, bacon and carrots - as noted by one of the Small Foxes, the Rabbits will require vegetables - and then to Bean's secret cider cellar. Here, they are nearly caught by the Beans' servant Mabel, and have an unpleasant conversation 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 for them daily and where none of them will need to worry about the farmers any more. 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."