He entered the Society of Jesus in 1596, and in 1602 left for India, which was his missionary field for the next 36 years.
Besides successfully catechizing and preaching, he left valuable descriptions of India in his letters to Christopher clavius and Christopher Grienberger, Jesuit mathematicians of the Roman College, descriptions that reveal a skill in cartography and mathematics. His Catena evangelica (seven volumes) became a useful exegetical guide for missionaries.
As visitor for the province of Japan and the vice-province of China in 1638, he learned the native languages well enough to discuss theology with the bonzes. Rubino became impressed with the advantages in adapting some of the Roman ritual to that of the Far Eastern religions, and wrote a defense of his views, Metodo della dottrina che i padri della Compagnia di Gesú insegnano ai neofiti nelle missioni della Cina con la risposta alle obiettioni di alcuni moderni che la impugnano (1641). Rubino wrote originally in Portuguese, this Italian version by G.F. Marini, was placed on the Index in 1660. This identification with the cause of the chinese rites followed him after death, when a calumnious book, Difesa del giudizio formato dalla Santa Sede Apostolica (Turin c. 1760), advocating an iconoclastic removal of crucifixes and other objects of the Roman rite from use in the East, was falsely ascribed to his authorship.
In 1643 Rubino and his companions reached the Japanese island of Satauma, where they were seized, they were brought to Nagasaki, and after imprisonment, died.