Hagen was born in Frankfurt am Main and raised in Augsburg, Germany where he attended the Anna Gymnasium. His father Wilhem Hagen was a pediatrician and later an important public health official in Germany. Ulrich Hagen graduated from the Ludwig Maximilian University of Munich with doctoral degrees in Medicine and Biology. In 1953, he was given a fellowship position at Heiligenberg Institute (one of the leading German institutes for Radiation Biology after WWII), which was then under the directorship of Hanns Langendorff.