Flanagan received his law degree, with distinction, from the University of Iowa in May 1988, where he received the American Jurisprudence Award for excellence in Bankruptcy Reorganizations. Flanagan served as a law clerk for The Honorable Chief Bankruptcy Judge Michael J. Melloy, United States Bankruptcy Court for the Northern District of Iowa, who now sits on the Eighth Circuit Court of Appeals. A 1985 graduate of Central College, a liberal arts college in Pella, Iowa, Flanagan was a four (4) year recipient of the Rolscreen Scholarship (the top academic scholarship awarded by Central College).