From 1988 to 1993, he was co-director, with Martin E. Marty, of the Fundamentalism Project, an international scholarly public policy study of religious movements throughout the world, funded by the American Academy of Arts and Sciences.

He has been a faculty member at the University of Notre Dame since 1994, where he became the John M. Regan Jr. Director of the Kroc Institute for International Peace Studies.

[4] Appleby was named the founding dean of the Keough School of Global Affairs at Notre Dame in 2014, where he served until June 30, 2024.

[8] He serves on the advisory board of The Charles and Margaret Hall Cushwa Center for the Study of American Catholicism at Notre Dame.

Gandhi Fellow of the American Academy of Political and Social Sciences[13] The Baptist Theological Union of the University of Chicago Divinity School named Appleby Alumnus of the Year for 2003.