In 1918-1919, Gulkowitsch went to Virbālis in Lithuania, where he headed a Hebrew-speaking basic school and was part of the Rabbinate. He then took up studying Medicine at the University of Königsberg, Germany (now Kaliningrad, Russia), but also attended classes in Philosophy and Theology, especially Old Testament. In 1922, he received both an Ph.D. and an M.A., the former with a work on the Kabbalah, and in 1924, and M.D., with a specialization in ophthalmology. In Königsberg, Gulkowitsch married Frieda Rabinowitz (27 February 1900 – Fall 1941); the couple would have two daughters.
Immediately after handing in his medical dissertation, however, Gulkowitsch had been invited by the University of Leipzig to take over the lecturership in Hebrew, Aramaic, and Talmudic Sciences from the renowned and recently deceased Israel Issar Kahan. Leipzig in Saxony was then the "mecca" of Oriental Studies in Germany, a very large and very highly regarded university (probably the best outside of Prussia). Gulkowitsch also became director of the Institute of Late Jewish Studies within the Old Testament division of the Divinity School. With his appointment, Gulkowitsch automatically became a German citizen.
At Leipzig, Gulkowitsch not only taught but continued studying there, with the eminent scholars available (especially in Islamic Studies, Near Eastern Studies, Ethiopian Studies, and Assyriology, as well as Philosophy with the eminent Theodor Litt) towards his Habilitation, which he attained in 1927. Continuing at Leipzig as Privatdozent (unsalaried senior lecturer who may be called to a professorship), he became, in 1932, Professor extraordinary (full professor without a chair) of Late Jewish Studies within the Faculty of Philosophy, the only such position within a German university. However, already a year later, in 1933, due to the Nazis’ rise to power and the Nuremberg race laws (which were, i.a., directed against Jews as civil servants, which in Germany professors are), he was dismissed from the University of Leipzig.
In the same year, however, the University of Tartu in Estonia, which had a very distinguished tradition of Oriental Studies and Hebrew, had opened, pushed by the local scholars and supported, i.a., by Albert Einstein - a new Institute of Jewish Studies – a remarkable and defiant feat for 1933, even for an independent country like Estonia proud of its minority rights laws. Gulkowitsch received the appointment as Professor and Chair of Jewish Studies and started teaching in Tartu in 1934. He attracted many high-calibre graduate students (mostly Jewish) and established an international publication series on Jewish Studies. Gulkowitsch taught in German; the Tartu institute was probably the only place in the world where scholarship on Jewish issues in German was possible to be upheld during times of the Holocaust. During his Tartu tenure, Gulkowitsch travelled as much abroad as was possible during that time, especially to Sweden (Uppsala University) and Britain (University of Cambridge).
When the Soviet Union invaded and annexed Estonia for the first time in 1940, anti-semitic pogroms started right away and many Jews were deported to Siberia. Gulkowitsch’s chair was abolished in 1941 and he himself dismissed. When the Nazis invaded Estonia in the same year, Gulkowitsch and, perhaps some weeks later, his entire family were – like almost 1,000 Estonian Jews that had not been deported and remained there – murdered by the Nazis.
The irrational-mystic approach to the study of religion also has its proponents (one could mention the tradition of Rudolf Otto and his classic The Holy (1917) here), but in the Comparative Religion field, Gulkowitsch’s approach, if somehow modified, could today be considered mainstream. This is less so within Jewish Studies (and the study of that discipline), partially for historical reasons, because the rationalism of Gulkowitsch’s style seemed to some unduly accommodationist to non-Jewish principles and systems of thought and too critical of its mystic traditions (it will be noted that Gulkowitsch indeed demystifies the Kabbala and the Talmud and is very critical of Chassidism). Thus, Jewish Studies scholars like Gerschom Sholem have criticized, and continue to criticize, Gulkowitsch’s work.
Because many of Gulkowitsch’s writings after 1933 were published in German in Estonia, they were actually not very well distributed and did not become part of the scholarly discourse of Jewish Studies, although they are of an extremely high quality and put Gulkowitsch clearly at the forefront of his area. Recent efforts to republish his most significant works with Germany’s leading publisher of Judaica, Mohr Siebeck in Tübingen, failed in 2005, after agreement with the press had already been reached, due to unknown reasons on the publishers' side.