Bonheur was born in Bordeaux, France, on 22 March, 1822. She was the eldest of a family of four artists, of whom her brother Isidore was best known. Her father, Raymond Bonheur, was a drawing master, with whom she studied in Paris; she also studied with Leon Cogniet and sketched at the Paris Zoo and at slaughterhouses on the outskirts of the city. She was primarily a painter, but was also known for her animalier sculpture, of which at least seven models were cast in bronze by her brother-in-law, the well-known founder Hippolyte Peyrol. She began exhibiting at the Paris Salon in 1841, showing drawings of rabbits and sheep in that year. In 1845 she received a third class medal, then a gold medal in 1865. She and her companion, Nathalie Micus, moved to By, near Fontainebleau, in 1859, where she lived for the remainder of her life; Micus died in 1889, after which Bonheur did little work. In 1893 she was created an Officer of the Legion of Honor.
Bonheur died at By, France, in 1899.