Janssen specialises in sixteenth and seventeenth-century Dutch history, and publishes on political and religious culture and the history of migration. He is currently completing a book on refugees and religious radicalisation during the Dutch Revolt (The Dutch Revolt and Catholic Exile in Reformation Europe), the writing of which has made him particularly interested in transnational approaches to Dutch history. In the years ahead he wishes to focus, among other things, on the influence of international migration on the cultural history of the Dutch Golden Age.

Since 2010, Janssen has been working as a Special Lecturer in Early Modern Dutch History at the University of Oxford and as a Fellow at Corpus Christi College. Previously, he was a lecturer at the University of Cambridge. In 2007, he was awarded a Veni grant by the Netherlands Organisation for Scientific Research (NWO). Janssen is the author of Princely Power in the Dutch Republic: Patronage and William Frederick of Nassau (1613-64) (Manchester University Press, 2008). Together with Alexandra Bamji and Mary Laven, he is the editor of the Research Companion to the Counter-Reformation (Ashgate, 2013). Janssen has also published in the Journal of Ecclesiastical History, Renaissance Quarterly, Sixteenth Century Journal and History.