Magnes graduated from Oakland High School as a valedictorian in 1894. He then studied at the University of Cincinnati, where he gained a degree of notoriety in a campaign against censorship of the "Class annual" of 1898 by the university faculty. He graduated from the University of Cincinnati with an A.B. in 1898. He also attended rabbinical seminary at Hebrew Union College, and was ordained a rabbi in June 1900. He then went to study in Germany. He studied Judaism at the Berlin Jewish College, Lehranstalt, and pursued his doctoral studies at Berlin University, where he studied under Friedrich Paulsen and Friedrich Delitzsch, and at the University of Heidelberg. It was while he was in Berlin that he became an ardent Zionist. He spent time traveling through Eastern Europe, and visited Jewish communities in Germany, Poland, and Galicia. In December 1902, he received a PhD in Philosophy from the University of Heidelberg, and returned to the United States in 1903.