Jan-Werner Müller studied at the Free University, Berlin, University College, London, St. Antony’s College, Oxford, and Princeton University. From 1996 until 2003 he was a Fellow at All Souls College, Oxford; from 2003 until 2005 he was Fellow in Modern European Thought at the European Studies Centre, St. Antony’s College. Since 2005 he has been teaching in the Politics Department, Princeton University.

Müller has been a visiting fellow at the Wissenschaftskolleg, Berlin, Collegium Helsinki, the Institute for Human Sciences in Vienna, and a number of other institutes; he has also been a Member of the School of Historical Studies, Institute of Advanced Study, Princeton.  He has  taught as a visiting professor at the Ecole des Hautes Etudes en Sciences Sociales, Paris, the Ludwig Maximilians-Universität in Munich, American University, Beirut, the Law School of Haifa University, the Humboldt Universität in Berlin, and the Institut d'Etudes Politiques, Paris.  He has delivered the Carlyle Lectures at Oxford and the Tanner Lectures at Cambridge; he is scheduled to deliver lectures at the Collège de France in 2024.

Müller is a co-founder of the European College of Liberal Arts, Berlin (ECLA; today: Bard Berlin), Berlin, Germany’s first private, English-speaking liberal arts college, for which he served as founding research director. He maintains a strong interest in international teaching and research initiatives centered on the liberal arts.

Müller is the author of Another Country: German Intellectuals, Unification and National Identity (Yale UP, 2000; Chinese translation), A Dangerous Mind: Carl Schmitt in Post-War European Thought (Yale UP, 2003;German, French, Japanese, Greek, and Chinese translations); he is also the editor of Memory and Power in Post-War Europe: Studies in the Presence of the Past (Cambridge UP 2002) and German Ideologies since 1945: Studies in the Political Thought and Culture of the Bonn Republic (Palgrave 2003). His book Constitutional Patriotism was published by Princeton University Press in 2007 (Chinese, Serbian, Greek, Turkish, and Korean translations); an expanded and revised German edition was published by Suhrkamp in 2010.

His history of political thought in twentieth-century Europe, Contesting Democracy, was published by Yale University Press in the summer of 2011 (Italian, French, Danish, German, Swedish, Russian, Polish, Chinese, Danish, and Serbian translations). His book Was ist Populismus? was published by Suhrkamp in April 2016; the University of Pennsylvania Press brought out an American version in September of 2016; the book has been published or is scheduled to be published in more than twenty other languages so far. Mueller's book Furcht und Freiheit: Für einen anderen Liberalismus was published by Suhrkamp in 2019 and won the Bavarian Book Prize. 2021 saw the publication of Democracy Rules by FSG in the US and Penguin in the UK. 

His public affairs commentary and essays have appeared in the London Review of Books, the New York Review of Books, Foreign Affairs, The Guardian, the New York Times, and Project Syndicate.