Friedrich Jürgen Baethgen (30 July 1890 – 18 June 1972) was a German historian born in Greifswald. He specialized in medieval studies and in history of the papacy.
He studied history at the Universities of Berlin and Heidelberg, earning his doctorate in 1913 under the guidance of Karl Hampe (1869–1936) with a thesis on Pope Innocent III. Afterwards, he was a lecturer and associate professor at Heidelberg, then becoming a professor of history at the University of Königsberg (from 1929). From 1939 to 1948 he taught classes in Berlin.
In 1927, Baethgen was appointed second secretary at the German Historical Institute in Rome. From 1948 to 1959, he was president of the Monumenta Germaniae Historica, and from 1956 to 1964, he was president of the Bayerischen Akademie der Wissenschaften (Bavarian Academy of Sciences). He never married.