He obtained a 3rd cycle thesis scholarship that he led under the direction of Robert Schilling and which he supported in 1972 in Strasbourg.
From 1977 to 1983, he was an assistant at the University of Lille-3, then became director of studies at the École pratique des Hautes Études (EPHE), section of religious sciences.
In 1987, he defended his doctoral thesis, Romulus et ses frères : Le culte des frères arvales, modèle du culte public dans la Rome des empereurs (‘Romulus and his brothers: The worship of the Arval Brethren, a model of public worship in imperial Rome’).
He is codirector of the Revue d'histoire des religions and member of the board of editors of numerous journals: Archives de sciences sociales des religions, Archiv für Religionsgeschichte (Teubner, Stuttgart-Leipzig), Potsdamer Althistorische Beiträge, Historia [fr], Millenium and Mythos.
According to historian Jean-Louis Voisin, John Scheid "revolutionized [...] the study and approach of the Roman religion by insisting on the precise fulfillment of its rites and its civic character".