In 1987, Flanagan began his political career by being elected to the Maryland House of Delegates, representing District 14B, which covered parts of Montgomery and Howard Counties.
As a Republican member in the heavily Democratic House of Delegates, Flanagan served the role as Minority Whip from 1997 until 2001.
During Flanagan's tenure as Secretary from 2003 to 2007, Maryland obtained approval under the National Environmental Policy Act to begin construction of the Inter-county connector as a state of the art, congestion managed highway by developing a new environmentally sensitive design after two prior rejections by the EPA in 1983 and 1997.
In 2006, Baltimore Mayor, Martin O'Malley, defeated Bob Ehrlich in the gubernatorial election, thus ending Flanagan's tenure as the Secretary of Transportation.
From 2007 to 2009, Flanagan was a Senior Vice President with First Southwest Company, advising state and local governments regarding public private partnerships for transportation.
He has been a speaker on this topic in various forums including the John F. Kennedy School of Government, Study Group on Transportation Infrastructure.
In 2009, Flanagan co-authored "Emerging Trends in Surface Transport Concessions PPPs in the U.S." which was published in Investing in Infrastructure, a comprehensive research source on infrastructure funds, investment techniques, and financing challenges in the world's diverse market by PEI Media Ltd. Flanagan is a practicing attorney in Columbia, Maryland, focusing on business representation, litigation, government matters, and procurement law.