Daunton previously taught at the University of Durham and University College London, before moving to Cambridge in 1997. He was chair of the Faculty of History and of the School of Humanities and Social Sciences before he was elected to the Mastership of Trinity Hall in 2004, from which he retired in 2014. He was president of the Royal Historical Society from 2003 to 2007, which involved him in debates over the role of history in education. He was a trustee of the National Maritime Museum 2002-10, where he was active in discussions about how to interpret events in British history such as Trafalgar and the end of the slave trade. He is chair of the academic awards committee of the Leverhulme Trust and a Commissioner of English Heritage. Since 2012, he has been head of the School of the Humanities and Social Sciences. He continues to teach, write and research in modern economic history. His current project is a book on the economic government of the world since 1933.