Born in Palermo, Sicily, on December 6, 1538, he was the son of Federico II Gonzaga, Duke of Mantua, and Margaret Paleologa. His family was one of Italy's most prominent princely houses, known for their significant political influence and patronage of the arts.
Gonzaga pursued an ecclesiastical career from a young age. He was elevated to the rank of cardinal by Pope Pius IV on February 26, 1561, at the age of 22, and received the title of Cardinal-Deacon of San Nicola in Carcere.
Throughout his brief life, he held several important ecclesiastical positions. He served as Apostolic Administrator of the Diocese of Bovino from 1561 to 1562 and was appointed Bishop of Mantua in 1564, a position he held until his death. Additionally, he acted as administrator of the Diocese of Reggio Emilia from 1566.
Cardinal Gonzaga participated in the papal conclave of 1565–1566 that ultimately elected Pope Pius V. He died in Rome on January 6, 1566, at the young age of 27. His early passing cut short a promising career within the Church, but he remains a notable figure in the history of the Gonzaga family and the Papacy during the Counter-Reformation period.