He received his medical doctorate in 1867 from the University of Vienna, and after graduation worked as an assistant to Theodor Billroth.
In 1882 he performed the first successful operation of a pancreatic cyst via the external drainage technique that he developed.
Prior to Gussenbauer's method, attempts at pancreatic surgery yielded negative results.
Gussenbauer's external drainage procedure represented the first safe and effective solution for pancreatic cysts, and was widely used until the 1950s.
Following Billroth's first successful laryngectomy on 31 December 1873, Gussenbauer created an external vocal prosthesis (artificial larynx) for the patient.