Johann Joseph Scherer (18 March 1814 – 17 February 1869) was a German physician and chemist born in Aschaffenburg.

From 1836 to 1838 he practiced medicine in Wipfeld, afterwards relocating to the University of Munich, where he resumed his studies in chemistry.

In 1840 he worked in the laboratory of Justus Liebig (1803-1873) at Giessen, returning to Würzburg in 1842 as a professor of organic chemistry.

Beginning in 1852, with Rudolf Virchow (1821-1902) and Gottfried Eisenmann (1795-1867), he was co-editor of Karl Friedrich Canstatt’s annual reports, Jahresbericht über die Leistungen und Fortschritte der gesammten Medicin.

One of his better known publications was the 1843 book Chemische und Mikroskopische Untersuchungen zur Pathologie angestellt an den Kliniken des Julius-Hospitales zu Würzburg (Chemical and microscopic investigations of pathology performed at the Julius Hospital Clinic at Würzburg).