Flanagan was a prolific medallic artist. Among his more important works, he designed the official medal of the Panama-Pacific International Exposition of 1915. He later sculpted the Verdun Medal, a gift of the United States to France commemorating the World War I Battle of Verdun. The inscription on it reads, 'They Shall Not Pass', and the medal is found in the Lafayette Database of American Art in French National collections. Flanagan also created the first issue of the influential Circle of Friends of the Medallion series, 1909's "Hudson-Fulton Celebration", and contributed to the successor Society of Medalists series with his "Aphrodite-Swift Runners" medal of 1932.