Martin Stokhof studied philosophy and linguistics, and has published extensively on topics in formal semantics and pragmatics, and on the philosophy of Wittgenstein. He is co-author of a two-volume textbook on logic and formal semantics, which was translated into English, Spanish and Mandarin, and he wrote a widely-used textbook in philosophy of language. His current work is mainly on topics in the philosophy of linguistics.

From 1991 to 2011, he was associate editor for semantics and philosophy of language of Linguistics and Philosophy. He is a member of the editorial boards of a number of other leading international journals in the field. In 2006, he was elected member of the Dutch Royal Academy of Sciences, in 2007 he became a member of the Institut International de Philosophie, and in 2016 he was elected member of the Academia Europaea. 

He was scientific director of the Institute for Logic, Language and Computation from 1998 until 2004. From 2004 to 2010 he was chairman of the Humanities Council of NWO, the Dutch Science Foundation, and a member of the Standing Committee of the Humanities of the European Science Foundation. He was founding chairman of the HERA consortium, in which national funding organisations in the area of humanities co-operate in a European setting.