In 2001, Dougherty was the Democratic nominee in a special election to fill the State Senate seat vacated by Lacy Clay when Clay was elected to Congress in November 2000. Dougherty won the election with nearly 84% of the vote.
Upon his election to the Senate, Dougherty resigned his seat in the Missouri House of Representatives. He was succeeded by Mike Daus.
In 2002, Dougherty sought election to a full term in the State Senate. He was opposed by State Representative O.L. Shelton in the Democratic primary. Dougherty defeated Shelton in the primary election
, and was unopposed in the general election 
During his career in the Missouri House and Senate, Dougherty, a former social worker, has focused on issues impacting families and children. When the Democrats controlled the Missouri House, Dougherty served as chair of the Children, Youth and Families Committee.
Due to term limits Doughtery was unable to run for re-election in 2006. Jeff Smith won a heavily contested Democratic primary to replace Dougherty.