Born in Vienna, Ferdinand Junker graduated from the University of Vienna in 1854, qualifying in 1855 in obstetrics, surgery, and ophthalmology. He was assistant surgeon in the 1st Light Dragoons, before coming to England and, taking the MRCS in 1860, and establishing a practice at 56 Gower Street. He was physician to outpatients at the Samaritan Free Hospital for Women and Children until 1871, and he described his chloroform inhaler in 1867.  In 1871 he saw von Langenbeck using the Tredelenburg tube for operations on the larynx.

During the Franco-Prussian War of 1870, Junker was chief physician and director of the English Hospital, Saarbrücken, although his name disappears from the Medical Directory between 1873 and 1882.  During some of this time he was chief physician and director of the medical school at Kyoto, Japan, arriving at Osaka on 25 August 1872, and leaving Kyoto on 12 March 1876.  His service was apparently regarded as unsatisfactory. Despite this he became interested in Japanese art and literature and wrote monographs and translated classical dramas into German.

He last appears in the Medical Directory in 1901. He probably died before 1902, although no obituary has been found.