While still a child, he was taken to Seville by his parents, who were Marranos. He studied philosophy at Alcalá de Henares and became teacher of metaphysics at the University of Salamanca. Later he devoted himself to the study of medicine, and became a popular practitioner in Seville, and physician in ordinary to the duke of Medina-Celi and to a family nearly related to the king.
When married and father of a family, De Castro was, at the instigation of a servant whom he had punished for theft, denounced to the Inquisition as an adherent of Judaism, and thrown into a dark and narrow dungeon, where he remained for three years, subjected to the most frightful tortures. As he persistently denied the charge, he was finally released, but compelled to leave Spain and to wear the sambenito, or penitential garment, for two years. He thereupon went to Toulouse, where he became professor of medicine at the university, at the same time receiving from Louis XIV the title of councilor; but, weary at last of hypocrisy and dissimulation, he went to Amsterdam about 1666, and there made a public confession of Judaism, adopting the name "Isaac." In that city De Castro continued the practice of medicine, and soon became a celebrity, being elected to membership in the directory of the Spanish-Portuguese congregation and of several academies of poetry. Esther, his wife, died on July 5, 1712.