Francis Willughby (November 22, 1635 - July 3, 1672) was an English ornithologist and ichthyologist.

He was the son of Sir Francis Willughby, and was born at Middleton Hall, Warwickshire. He studied at Sutton Coldfield school and Trinity College, Cambridge.

At Cambridge he was taught by the naturalist John Ray. In 1662 they travelled to the west coast of England to study the breeding seabirds. Between 1663 and 1666 they toured Europe together, travelling through the Netherlands, Germany, Switzerland and Italy. They separated at Naples and Willughby returned home via Spain. On returning to England they made plans to publish the results of their studies. Willughby died during the preparation of this work, but Ray published Willughby's Ornithologia libri tres in 1676, with an English edition two years later. This is considered the beginning of scientific ornithology in Europe, revolutionizing ornithological taxonomy by organizing species according to their physical characteristics. Ray also published Willughby's De Historia piscium (1686).

In 2003 Willughby's scientific study of games was published (under the name Francis Willughby's Book of Games), making generally available for the first time indepth descriptions of a number of seventeenth century games. It was the first such work in the English language, and is comparable to the Spanish Libro de los juegos.

The Willughby family seat, Wollaton Hall, now owned by the City of Nottingham, houses Willughby and Ray's natural history collection of stuffed animals and birds.