Stokhof held a number of administrative functions, including scientific director of the Institute for Logic, Language and Computation (ILLC), chairman of the humanities board of Netherlands Organisation for Scientific Research (NWO), chairman of the HERA-consortium, chairman of the KNAW-NVAO accreditation committee for research masters, and of the KNAW-NWO China committee.

Since 2014 he is member of the scientific council of the European Research Council (ERC). Currently he is vice-president and coordinator of the Social Science and Humanities domain.