During the administration of President George H. W. Bush, he was appointed at the Department of Justice as Assistant Attorney General for the Office of Legal Counsel, from 1990 to 1992.
After the 2000 United States presidential election, Flanigan served as a lawyer in the case of Bush v. Gore over the methods and procedures used in counting the Florida vote.
During the administration of President George W. Bush, he served as Deputy White House counsel to Alberto Gonzales, until December 2002.
In that role, Flanigan was a principal legal advisor for the President, the Attorney General, and the heads of the executive branch agencies.
[4] A member of the Federalist Society, he is currently Chief Legal and Compliance Officer and Corporate Secretary at Cancer Treatment Centers of America.