When he returned to Italy, he was made professor of anatomy at the University of Pavia in 1783, on the strong recommendation of Emperor Joseph II.

His lectures were so popular with students that Emperor Joseph II commissioned Leopoldo Pollack to build a new anatomic theater, now called Aula Scarpa, inside the Old Campus of the University of Pavia.

[3] In May 1791, he was elected a Fellow of the Royal Society on account of being the "Author of some ingenious observations on the Ganglions of the Nerves, on the structure of the organs of hearing and smell, and other subjects of anatomy and Physiology"[4] In 1805, Napoleon was made King of Italy.

He was informed that the doctor had been dismissed because of his political opinions and his refusal to take oaths, whereupon Dr. Scarpa was restored to his position as the chair.

As an incredible and ethically dubious act of homage to the great scientist, the head of the anatomist was removed and exhibited in the Institute of Anatomy.