Johann Schnitzler, son of a carpenter, was a native of Nagykanizsa in Hungary (then part of the Austrian Empire).
He studied medicine at the universities of Budapest and Vienna, where in 1860 he earned his medical doctorate and from 1863 to 1867 worked as an assistant to Johann von Oppolzer (1808–1871).
He married Luise Markbreiter (1838–1911), daughter of the renowned Viennese doctor Philipp Markbreiter, and they had four children: the doctor and playwright Arthur Schnitzler (1862–1931); Joseph Emil, who died shortly after his birth in 1864; Julius Schnitzler (1865–1939), who also was a surgeon and professor; and Gisela (1867–1953).
Schnitzler was a pioneer of modern laryngology, the author of numerous works and specialist articles on diseases of the throat and larynx.
His reputation as laryngologist made him a sought after physician in theatre circles; likewise his son Arthur cared for celebrated actors like Adolf von Sonnenthal and Charlotte Wolter, and numerous singers of the Viennese Court Opera.