Stokhof held a large number of administrative functions at the University of Amsterdam, and in national and European bodies.

At the Institute for Logic, Language and Computation (ILLC) he was deputy scientific director from 1991 to 1996, and scientific director from 1998 to 2004 . From 2003 to 2009 he served on the humanities board of Netherlands Organisation for Scientific Research (NWO) (from 2004 to 2009 as chairman); he was on the board of the HERA-consortium (chair 2003–2007, member 2007–2009), and was member of the Standing Committee for the Humanities chairman of the European Science Foundation (2005 – 2009). He also chaired the KNAW-NVAO accreditation committee for research masters (2010 – 2015), and the KNAW-NWO China committee (2011 – 2021).

From 2014 to 2019 Stokhof was member of the scientific council of the European Research Council (ERC). He chaired the ERC’s Open Access working group, and was a member of various other working groups and committees. From 2017 to 2019 Stokhof served as vice-president of the ERC and coordinator of its Social Science and Humanities domain.

Information about these and other functions can be found in Stokhof’s curriculum vitae.