In 1922 Viktor Christian obtained his habilitation in the Philosophy Faculty of the University of Vienna with a thesis "Semitic with special account of cuneiform writing". He was made an extraordinary professor in 1924 and six years later an ordinary professor of old Semitic philology and Near Eastern archaeology. He was a member of the "Bärenhöhle" (bears' cave), an antisemitic network of professors that sought to prevent the appointment and habilitation of Jewish and/or left-wing academics at the University of Vienna. He applied to join the NSDAP in 1933 but was not given a membership number. After being dismissed from the university for his National Socialist activity in 1934, he was reappointed in 1936 under the July agreement. In May 1938 he once again applied for membership of the NSDAP and was given the membership number 6127801. In November he also joined the SS (1943 SS‑Sturmbannführer).

After the annexation, he became head of the Department of Near Eastern Studies of the University of Vienna and member of the Academy of Sciences. He was temporary dean of the Philosophy Faculty before being confirmed in this position in April 1939. In 1938 he was also interim head of the Ethnology and Anthropology Institutes of the University of Vienna. To obtain "Jewish skeleton material" for anthropological research, in 1941 he directed the exhumation of Jewish graves at Währing cemetery. Thanks to his connections with National Socialist circles, he also became head of the SS-Ahnenerbe teaching and research centre for Near Eastern studies. From June 1943 until 1945 he was also head of the Vienna section of the National Socialist Altherrenbund (League of Alumni). He reached the highpoint of his career shortly before the end of the war, when in April 1945, after two years as pro‑rector, he became rector of the University of Vienna, albeit only for a few days. From mid-May 1945 to July 1947, he was interned in various camps and in June 1945 was dismissed by the Staatsamt für Volksaufklärung, für Unterricht und Erziehung (State Department for Public Enlightenment, Schools and Education) because of his membership of the NSDAP. The dismissal was transformed into retirement with a pension as a result of the 1950 amnesty legislation. Following a festschrift in honour of his seventieth birthday in 1955, he was awarded the Goldenes Doktordiplom (Golden Doctoral Diploma) of the University of Vienna in 1960.

During the Nazi era, Viktor Christian repeatedly endeavoured to obtain books expropriated from their Jewish owners for the Department of Near Eastern Studies. He was successful in the case of the SS‑Ahnenerbe but not so in other cases. He attempted to acquire the library of the Albanologist Norbert Jokl (1877–1942) for the University of Vienna but had to give way to the director general of the National Library Paul Heigl (1887–1945). Altogether, the Department of Near Eastern Studies acquired over 8,000 publications on permanent loan from the Ahnenerbe from the Jewish communities in Burgenland (Kittsee, St. Peter, Frauenkirchen and Lackenbach), from the private collections of Samuel Krauss (1866–1949) and Ludwig Feuchtwanger (1865–1947) and from the Zentralstelle für jüdische Auswanderung (Central Office for Jewish Emigration) and the Völkerkundemuseum (Museum of Ethnology) in Vienna, which had been expropriated by the Nazis. After the war most of them were given to the IKG Wien (Vienna Jewish Community) and subsequently sent to Israel.