Thompson was raised as a Catholic and obtained a bachelor of arts from Duquesne University, in Pittsburgh, Pennsylvania, United States, in 1962. After a year in Oxford, he moved to Tübingen, where he studied for 12 years with Kurt Galling and Herbert Haag. In the meantime, he was instructor in theology at Dayton University (1964–65) and assistant professor in Old Testament studies at the University of Detroit (1967–69). He then studied Catholic theology at the University of Tübingen; his dissertation, "The Historicity of the Patriarchal Narratives: The Quest for the Historical Abraham", was completed in 1971, but rejected by the Catholic faculty (one of his examiners was Joseph Ratzinger, then Tübingen's Professor of Systematic Theology and later Pope Benedict XVI). Thompson then considered submitting his dissertation to the Protestant faculty, but left Tübingen in 1975 without a degree. The rejected dissertation was published in 1974 by De Gruyter Press. The work, together with John Van Seters' "Abraham in History and Tradition", became one of the pioneer works of biblical minimalism.