Ferrari worked in Rome (1617-18), Parma (1619-23), and possibly in Modena at some time between 1623 and 1637. He created music and libretti in Venice and Bologna, 1637-44. Ferrari's Andromeda, with music by Francesco Manelli, was the first Venetian opera performed in a public theatre (in 1637). Subsequently he provided both the text and the music for two operas, both presented in Venice: La maga fulminata (1638) and Il pastor regio (1640). The 1641 Bolognese staging of the latter included, as its final duet, the text "Pur ti miro, pur ti godo," which was later reused, possibly with Ferrari's music, for the final duet in the surviving manuscripts of Monteverdi's L'Incoronazione di Poppea.

Ferrari went to Vienna in 1651, seving the emperor Ferdinand III. Upon returning to Modena in 1653 he was appointed court choirmaster. His post was eliminated in 1662 but reinstated in 1674, after which he served until his death. Many sources recount his virtuosity as a theorbo player.

None of his operatic music survives. Extant works include libretti, an oratorio, and three books of monodies under the title Musiche varie a voce sola (Venice 1633, 1637, 1641). Though the last were composed within a relatively short time span, they reflect the changing style of accompanied monody, from the emergence of recitar cantando (midway between song and speech) to the vocal style that is typical of mid-seventeenth-century opera, with a more distinctive melody and a clearer rhythm.