James W. Flanagan was born on December 27, 1935. He was awarded a Bachelors degree from Loras College in 1958, a Bachelor of Sacred Theology (1960) and a Licentiate of Sacred Theology (1962)from Gregorian University in Rome, and his Ph.D. from Notre Dame College in 1971. Flanagan came to archeology by way of biblical studies, research groups he chaired on the social scientific study of ancient Israel, and administrative and editorial positions within academic publishing. After completing his Ph.D. at Notre Dame University in 1971, he did post-doctoral research at the University of Michigan and Cambridge University in the fields of Near Eastern Studies and Social Anthropology and Archeology. He taught at Loras College (1964-1973), the University of Michigan (1973-1976), and the University of Montana (1976-1986)where he chaired the Religious Studies Department and served as Associate Director of Scholars Press. In 1986 Flanagan was appointed the Paul J. Hallinan Visiting Professor of Catholic Studies while on leave from the University of Montana. He retained that title for five years, remaining on leave from the University of Montana. In April, 1990 (effective July, 1991) he became Professor of Religion, with tenure, at CWRU. In March, 1991 (effective July, 1991) he became the Paul J. Hallinan Professor of Catholic Studies at CWRU and was made Paul J. Hallinan Professor of Catholic Studies, Emeritus in 2002. He died on September 1, 2015.

His earliest excavations included Tell Gezer (Israel), Babe dh-Dhra (Jordan), Tell Qarqur (Syria), and related field work in Saudi Arabia and North Yemen. With Willamette University Professor David W. McCreery, he launched the Tell Nimrin Project, an archeological expedition to the Jordan Valley, in 1985. At the request of the Jordanian Department of Antiquities, they organized a team to examine a town site in modern Shuna South that was being threatened by regional development. In 1986, a small team photographed and drew principal features of the mound as preparation for excavations to begin later. After 1989, Khair N. Yassine, University of Jordan, joined Flanagan and McCreery in administering the project. In 1989 and 1990, research teams of 20 to 25 U.S. faculty and students were joined in the field by professional archaeologists from the University of Jordan in order to pursue full excavation. The project excavated again in 1993, and returned to the field for the last time in 1995.

Beginning in 1996, Flanagan focused on the publication and presentation of data in a groundbreaking fashion via the then nascent world wide web. Virtual Nimrin presented findings of the Tell Nimrin Project though a collaboration with Case Western Reserve University and the Virginia Institute of Technology. It included electronic versions of field books, selected photos, and publishable drawings, as well as a comprehensive collection of reports and a selection of rare texts in archeology called the Etana Core Texts. Flanagan retired from active field work after the 1995 season at Tel Nimrin, and from Case Western Reserve University in 2002.