Josef Thenen was born on 21 August 1866 in Galati in present-day Romania into a Jewish merchant family. He had a sister Carolina and a brother Adolf. After attending the Leopoldstädter Communal-Real- und Obergymnasium he studied medicine at the University of Vienna from 1884 and obtained his doctorate in 1890. His first marriage was to Hermine Doctor from Náchod, Bohemia. The marriage was childless. After divorcing her, he married Isabella "Bella-Charlotte" Rottenberg from Galati in 1893. This marriage was also childless. He continued his training, first as an assistant physician at the General Hospital in Vienna at the clinics run by Hermann Nothnagel and Friedrich Schauta, and carried out a number of experiments at the pathology laboratory headed by Samuel von Basch. He was a member of the Internationales Komitee für das ärztliche Fortbildungswesen (International Committee for Continuing Medical Education) and was instrumental in the introduction of advanced training in Vienna and Lower Austria. In 1905, he was the first to suggest the administration of adrenaline as a treatment for shock, a therapy that is still used today. He is also regarded as the inventor of the catalytic oxygen bath. His insistence on liability insurance for doctors resulted in the founding in 1910 of the Unfall- und Haftpflichtversicherungs-Aktiengesellschaft Kosmos with himself as chairman of the board of administrators. In 1920 he was appointed Obermedizinalrat, and 1923 member of the Oberster Sanitätsrat (Supreme Health Council). From 1920 to 1936 he was president of the Wiener Ärztekammer (Vienna Medical Chamber). In 1928 he became Hofrat and member of the Federal Committee of the Austrian Red Cross Society. During all of this time he had an internal medicine practice at his apartment at Ferstelgasse 1 in the 9th district. In March 1938 his practice, according to his own statement, effectively ceased to exist.
After the annexation of Austria to Nazi Germany, Josef and Isabella Thenen were persecuted by the Nazi regime because of their Jewish origins. On 1 August 1939, Josef wrote to the head of the Städtische Sammlungen Wien that he had been given "notice to leave the apartment he had lived in for forty-six years in implementation of the Jewish laws" and that he therefore no longer had room for the plaster statue Gladiator and Conquered Slave by Viktor Tilgner, which he therefore proposed to "donate" to the museum. Thenen was paid a "token amount" of 100 Reichsmarks. On 16 October 1939 Josef and Isabella Thenen were registered as having left Vienna for Romania, the country of their birth. Isabella died on 1 July 1942, Josef on 15 January 1949 in Braila. Thenen's divorced first wife Hermine Doctor perished on 23 September 1942 probably during her transport from Theresienstadt to the Maly Trostinec extermination camp. The Wien Museum restituted the plaster statue in March 2012 to the legal successors of Josef Thenen.