[2] In 2002, Flanagan sought the assembly minority leader post, and was defeated 27–26 by fellow Republican Charles H.

[3][4] Before becoming temporary president and majority leader of the New York state senate, Flanagan served as the chairman of the senate standing committee on education and as a member of the committees on codes; corporations, authorities and commissions; finance; higher education; insurance; judiciary; rules and veterans, homeland security and military affairs.

The hearing series was called "The Regents Reform Agenda: 'Assessing' Our Progress" and was held on Long Island and in New York City, Syracuse, Buffalo and Albany.

[8] As senate majority leader, Flanagan pushed back on efforts to extend the statute of limitations for victims of child sexual abuse in New York state.

He did not allow the Child Victims Act,[9] a bill that had already passed the New York Assembly,[10] to come up for a vote in the senate in the 2017 spring session.

[16] In January 2020, Flanagan announced that he would be unavailable for the beginning of the 2019 session because he was seeking treatment for alcoholism in a residential program.