While in Egypt he was appointed by viceroy Mehmed Ali (1769-1849) as chair of anatomy and physiology at the medical school in Abuzabel, near Cairo.
Subsequently, he served as a professor of ophthalmology as well as director of the hospital at Kasr al Aini.
After the outbreak of the Franco-Prussian War, he moved to Pisa, where he worked as a private scholar until his death in 1882.
While in Egypt, Pruner dealt with the treatment of epidemics such as bubonic plague, cholera and typhoid fever.
In a book which he wrote in 1846 he claimed that Negro blood had a negative influence on the Egyptian moral character.