At the University of Berlin, he studied mathematics under Issai Schur, Edmund Landau, Ferdinand Georg Frobenius, and Friedrich Schottky; philosophy under Alois Riehl, Carl Stumpf and Ernst Cassirer; and physics under Max Planck.

At the University of Göttingen, he studied mathematics under David Hilbert, Edmund Landau, Hermann Weyl, and Felix Klein; physics under Voigt and Max Born; and philosophy under Leonard Nelson.

In 1912, the University of Berlin awarded him a Ph.D. in mathematics for a thesis, supervised by Landau, on the analytic number theory of binary quadratic forms.

After working privately for Hilbert for six months, Bernays and his family moved to Switzerland, whose nationality he had inherited from his father, and where the ETH Zurich employed him on occasion.

Bernays's collaboration with Hilbert culminated in the two volume work, Grundlagen der Mathematik (English: Foundations of Mathematics) published in 1934 and 1939, which is discussed in Sieg and Ravaglia (2005).