Born in Kedichem in 1962, Verhoef received his PhD in computer science at the University of Amsterdam in 1992 under supervision of Jan Bergstra with the thesis "Linear unary operators in process algebra.

"[1] Verhoef had done his graduate work at the Programming Research Group of the University of Amsterdam, where in 1990 he had published his first report "On the register operator."

Early 1990s he joined the Department of Mathematics and Computing Science of Eindhoven University of Technology.

With Alban Ponse and Bas van Vlijmen, Verhoef initiated the first two International Workshops on the Algebra of Communicating Processes in 1994 and 1995.

In 1996/97 he returned to Programming Research Group of the University of Amsterdam, where he started focussing on Reverse engineering, the "theory and practice of recovering information from existing software and systems.