Boll studied medicine in Bonn, Heidelberg and Berlin, and in 1870 worked at the physiological institute of Emil du Bois-Reymond (1818–1896) in Berlin. Later he became a professor at the University of Genoa, and from 1873 to 1879 was a professor of physiology in Rome. He died in Rome on 19 December 1879 at the age of 30.
Boll is remembered for the discovery of rhodopsin, when he noticed that the light-sensitive pigment in the rods of the retina had a tendency to fade in the presence of illumination. He published his findings in an article titled Sull'anatomia e fistologia della retina. On 12 November 1876, he reported his discovery to the Berlin Academy.
His name is associated with the eponymous "Boll cells", being described as basal cells located in the lacrimal gland. As a student of Max Schultze (1825–1874) at Bonn, he was the author of a significant histological treatise on dental pulp called Untersuchungen über die Zahnpulpa.