Yosef Kaplan was born and raised in Buenos Aires. In 1962 he immigrated to Israel. He studied at the Hebrew University of Jerusalem, majoring in Jewish History and Sociology. In 1979 he completed his PhD in Jewish History, writing a thesis on Isaac Orobio de Castro and His Circle. He is Bernard Cherrick Professor of Jewish History at the Hebrew University of Jerusalem. He was fellow at the Institute for Advanced Study, The Hebrew University of Jerusalem; visiting professor at Yale University; fellow at the Royal Institute for Advanced Study in Wassenaar (The Netherlands); Associated Director of Research at the École des Hautes Etudes en Sciences Sociales, Paris; Goldsmid Visiting Professor at University College London; Visiting Scholar at Wolfson College, Oxford; Associated Director of Research at the École Pratique des Hautes Etudes, Sorbonne, Paris; Visiting Fellow at All Souls College, Oxford; member of the School of Historical Studies, The Institute for Advanced Study, Princeton. He was chairman of the Historical Society of Israel and member of the editorial board of the historical quarterly Zion. He was one of the founders of the School of History at the Hebrew University and its second Director. In 2004 he was elected member of the Israel Academy of Sciences and Humanities and since October 2013 he is chair of the Humanities Division. Between 2009-2013 he was the Chairman of the World Union of Jewish Studies. 

In 2012 he was awarded an Advanced Grant from the European Research Council (ERC) for a project on Religious and Cultural Changes in the Western Sephardi Diaspora in the Early Modern Period.

In 2013, Prof. Kaplan was awarded the Israel Prize for his work on the history of Jewish People.

His publications include: From Christianity to Judaism: The Story of Isaac Orobio de Castro (Hebrew: Jerusalem 1982; English version: Oxford 1989); Judíos Nuevos en Amsterdam (Barcelona 1996; French version Paris 1999); An Alternative Path to Modernity (Leiden 2000; enlarged Hebrew version, Jerusalem 2002). He has edited, among others, Fins des Siècle – End of Ages (Hebrew, Jerusalem 2005); The Dutch Intersection (Leiden and Boston 2008).