Van der Vegt studied chemical engineering and received his PhD from the University of Twente in 1998 on a study of methods for calculating thermodynamic and transport properties of small molecules in polymer membranes based on computer simulations. From 1998 to 2002, he was a lecturer at the University of Twente. Following this, he worked as a postdoctoral researcher at ETH Zürich with Wilfred F. van Gunsteren from 2002 to 2003. He then led a research group at the Max Planck Institute for Polymer Research, Mainz, Germany. In 2009, he was appointed as a full professor for computational physical chemistry at the Technische Universität Darmstadt.