[8] On February 1, 2009, Murphy was chosen by a unanimous vote of ten Democratic county chairs to be their party's nominee for 2009 special election to fill Gillibrand's seat in the House.

[9][10] Murphy ran against Republican nominee Jim Tedisco from Schenectady, who, until April 2009, was the Minority Leader of the New York State Assembly.

[12][13] However, by April 24, after re-tallies and absentee ballot counting, Murphy was ahead by 399 votes,[14] and Tedisco conceded the election.

[17] Murphy opposed the Stupak Amendment, which proposed to restrict federal funding and subsidies for plans that cover elective abortion.

In December 2010, Murphy voted for the Protecting Students from Sexual and Violent Predators Act,[20] which require criminal background checks for school employees and prohibits the employment of school employees who refuse to consent to a criminal background check, make false statements in connection with one, or have been convicted of one of a list of felonies or any other crime that is a violent or sexual crime against a child.