Born in Mantua, he was the eldest son of Duke Vincenzo I and Eleonora de' Medici.

[1] In 1607, Claudio Monteverdi dedicated his opera L'Orfeo to Francesco.

The title page of the opera bears the dedication "Al serenissimo signor D. Francesco Gonzaga, Prencipe di Mantoua, & di Monferato, &c." Francesco became Duke upon his father's death on 9 February 1612.

He died at Mantua on 22 December 1612 without male heirs.

He was succeeded by his brother Ferdinand; however, Charles Emmanuel I, Duke of Savoy, the father of Francesco's wife Margaret of Savoy, disputed this, leading to the War of the Montferrat Succession (1613–1617).