Strayhorn served two terms as Comptroller beginning in 1998. She received more votes than any other Republican on the statewide ballot in her 2002 bid for re-election. After the race, Strayhorn began criticizing Gov. Perry for his stance on state spending and school finance. In June 2003, Strayhorn announced her candidacy for governor. She faced incumbent Gov. Perry, Democratic challenger Chris Bell, and independent Kinky Friedman in the 2006 election. Strayhorn finished third behind Perry and Bell, drawing 18 percent of the vote.
Strayhorn was involved in Travis County politics before running for statewide office. She was the first woman to serve as mayor of Austin and the first female president of the Austin School Board. Strayhorn made failed bids for the U.S. House in 1986 and for the Texas Railroad Commission in 1992. She was elected to the Railroad Commission in 1994 and re-elected in 1996 and 1998.