The first mention of Fonyód was in a letter of Saint Ladislaus from 1082, as the village Funoldi. In 1232, the village was included into the lands of the Tihany Abbey. Maps from the 14th century show Fonyód as an island (with Balaton being larger), with a castle. The castle was occupied and destroyed in 1575 during the Turkish invasion, with no one living in the village by 1580. After the Turkish occupation, Fonyód remained uninhabited until the 19th century.

The construction of a railway around Lake Balaton greatly contributed to the village's development. By 1900, Fonyód had become a holiday resort, and by 1910 over a thousand visitors were arriving each year.

Fonyód attained town status in 1989.