[1] In 1867 he obtained his doctorate from the University of Würzburg, and shortly afterwards was an assistant at the internal medicine clinic in Greifswald (1867–68).
Later he studied with ophthalmologist Albrecht von Graefe (1828–1870) in Berlin, then subsequently took an extended scientific trip to London, Edinburgh and Paris.
After returning to Germany, he worked with his older brother, Alexander Pagenstecher (1828–1879), at the latter's eye clinic in Wiesbaden.
In her private journal she wrote: Pagenstecher is remembered for advancing his brother's pioneer work with intracapsular cataract extraction, of which he described in the monograph Die Operation des grauen Stars in geschlossener Kapsel.
With Carl Genth (1844–1904), he was co-author of Atlas der pathologischen Anatomie des Augapfels (Atlas of the Pathological Anatomy of the Eyeball), a book that was later translated into English by neurologist William Richard Gowers (1845–1915).