A professor of medicine at the universities of Würzburg (1824–33), Zürich (1833–40), and Berlin (1840–59), Schönlein was the first to use the microscope in conjunction with chemical analyses of urine and blood in the diagnosis of disease. He found and described (1839) the fungus (Achorion schonleinii) responsible for the skin disease favus and coined the term hemophilia (1828).

Schönlein was the first to describe the minute hemorrhages of the skin occurring in cases of anaphylactoid (allergic) purpura (Schönlein–Henoch purpura) and purpura rheumatica (Schönlein's disease; 1837), characterized by the appearance on the skin of small purple spots, by swelling, pain, and tenderness of joints, and frequently by swelling of the hands, feet, or eyelids.