Porto-Novo was probably founded in the late 16th century. It got its name from the Portuguese, who built a trading post there in the 17th century in order to ship African slaves to the Americas. The Kingdom of Porto-Novo accepted French "protection" in 1863 in order to fend off British encroachment. However, the neighboring Kingdom of Abomey resented the French presence, and war broke out. In 1883 the French navy landed at Porto-Novo and Cotonou, and Porto-Novo was incorporated into the French colony of Dahomey. In 1900 it was made Dahomey's capital.
The Institute of Higher Studies of Benin is located in the city.