Josef Breuerwas the son of Leopold Breuer (1791-1872), a liberal Jewish teacher of religion in Vienna. After the death of his mother when he was four years old, he was raised by his maternal grandmother. At the age of eight he entered the Akademisches Gymnasium of Vienna, where he passed the Abitur – high school graduation – in 1858. He then attended the University of Vienna for one year of general studies, before entering the university's medical school in 1859. He graduated in l864.
After defending his doctoral thesis in 1867, Breuer immediately became assistant to the internist Johann Ritter von Oppolzer (1808-1871) at the medical clinic in Vienna. In this position he undertook research on the physiological questions of temperature regulations of respiration.
When Oppolzer died in 1871 Breuer relinquished his assistantship and entered private practice. In this period he made epoch-making investigations into the anatomy and function of the inner ear, describing what is now known as the Mach-Breuer flow or shift theory of the endolymph of the inner ear. This research was the basis for his habilitation for internal medicine in 1875, when he received the "venia legendi" – the permission to teach as Privatdozent.
He gave up his venia legendi ten years later, probably both because of the high demands of his practice, and because he felt he had been improperly denied access to patients for teaching purposes.