Güterbock had to leave Germany three years after the Nazis came to power. He followed in the footsteps of his doctoral supervisor Benno Landsberger and emigrated to Turkey, where he held the post of Professor of Hittite Studies in Ankara until 1948. Here he met his future wife Franziska Hellmann, who had emigrated from Würzburg with her parents. Their two sons Walter Michael and Thomas Martin Güterbock were born in Ankara. In 1949, Güterbock settled in Chicago, where he taught at the University of Chicago's Oriental Institute. Güterbock remained active even after his retirement, for example as co-editor of the “Chicago Hittite Dictionary”. Along with a large number of contributions to academic journals, his works included Siegel aus Boghazköy (Seals from Boghazköy) (B.-Frohnau: self-published by ed. Dr. E. F. Weidner 1940–42) and Kumarbi: Mythen vom churritischen Kronos aus den hethitischen Fragmenten zusammengestellt, übersetzt und erklärt (Kumarbi: Myths of the Hurrian Cronos compiled from the Hittite fragments, translated and explained) (Zurich; New York: Europaverl. 1946). Güterbock received numerous awards and honours; in 1959, for example, he was named the Tiffany and Margaret Blake Distinguished Service Professor of the Oriental Institute at the University of Chicago. He also received honorary doctorates from the Free University of Berlin, the University of Uppsala and the University of Ankara.

Hans Gustav Güterbock's estate contains a large bundle of letters, e.g. from Kurt Bittel, Johannes Friedrich, Albrecht Goetze, Benno Landsberger and Ernst F. Weidner, together with numerous family letters, some dating from his time in exile; personal documents such as certificates, passports, photographs, notebooks, address books and family documents; a large number of photographs of landscapes and excavation sites, e.g. in Boghazköy, Istanbul, Karalar and Konya; and some specimen copies of his academic works and autobiographical writings.