Jan de Boer has been associated with the University of Amsterdam since 2000 as Professor of Theoretical Physics. Between 2010 and 2015 he was education director of the Graduate School of Science. He also leads the Institute for Theoretical Physics Amsterdam (ITFA), part of the Institute of Physics.
He was also one of the founders of GRAPPA research centre. From 2015 until 2016, Jan de Boer was in the executive board of FOM and from 1 January 2017 in the board of the Netherlands Organisation for Scientific Research - NWO Domain Science (ENW). Jan de Boer is looking forward to strengthen the relation between the NWO Domain Science and the eScience Center.