Barendregt studied mathematical logic at Utrecht University, obtaining his Masters in 1968 and his Ph.D. in 1971, both cum laude, under Dirk van Dalen and Georg Kreisel. After a postdoctoral position at Stanford University, he taught at Utrecht University.
Since 1986, Barendregt has taught at Radboud University Nijmegen, where he now holds the Chair of Foundations of Mathematics and Computer Science. His research group works on Constructive Interactive Mathematics. He is also Adjunct Professor at Carnegie Mellon University, Pittsburgh, USA. He has been a visiting scholar at Darmstadt, ETH Zürich, Siena, and Kyoto.