Born in Acquapendente, Latium, Fabricius studied at the University of Padua, receiving a Doctor of Medicine degree in 1559 under the guidance of Gabriele Falloppio.

[4] Julius Casserius (1552–1616) of Piacenza was among Fabricius' students,[6] Anselmus Boetius de Boodt (1550-1632) also received his lessons there in 1586.

[6] By dissecting animals, Fabricius investigated the formation of the fetus, the structure of the esophagus, stomach and intestines, and the peculiarities of the eye, the ear, and the larynx.

A manuscript entitled De Formatione Ovi et Pulli, found among his lecture notes after his death, was published in 1621.

Marco Aurelio Severino (1580–1656), a skilful surgeon and anatomist, performed at least one tracheotomy during a diphtheria epidemic in Naples in 1610, using the vertical incision technique recommended by Fabricius.