The city was created in 1250 by count Bernardino of Cunio after a flood which had destroyed his castle at Donigallia.

When the Duchy of Ferrara was annexed to the Papal States (1598), the fief was elevated to a marquisate, which in 1622, after a long struggle with the Corelli family, was acquired by the Calcagnini.

During World War II, as part of the Spring 1945 offensive in Italy, Fusignano was for four months on the front line, and reduced to ruins.

One soldier Ali Haidar was awarded the Victoria Cross for his actions here during World War II.

In the church of San Savino the ancient sepulchre of the namesake saint, one of the first evangelizers of Romagna, can be seen: however, the relics it contained were transferred by Astorre II Manfredi to a chapel in the Cathedral of Faenza.