Phelps ran in various Kansas Democratic Party primaries five times, but never won. These included races for governor in 1990, 1994, and 1998, receiving about 15 percent of the vote in 1998. In the 1992 Democratic Party primary for U.S. Senate, Phelps received 31 percent of the vote. Phelps ran for mayor of Topeka in 1993 and 1997.
Phelps supported Al Gore in the 1988 Democratic Party presidential primary election. In his 1984 Senate race, Gore had opposed a "gay bill of rights" and stated that homosexuality was not something that "society should affirm"), a position he had changed by 2000 when he had the support of homosexual advocacy groups for his presidential campaign. Phelps has stated that he supported Gore because of these earlier comments. According to Phelps, members of the Westboro Baptist Church helped run Gore's 1988 campaign in Kansas.
During the 1992 presidential campaign, Phelps criticized Hillary Rodham Clinton during a speech he gave endorsing Bill Clinton's presidential campaign at the University of Kansas on October 14, 1992. In 1996 Phelps and the Westboro church opposed Clinton's re-election because of the administration's support for gay rights. The entire Westboro congregation picketed a 1997 inaugural ball, denouncing Vice President Al Gore as a "famous fag pimp" (Gore had changed his positions on gay rights since 1984). In 1998, Westboro picketed the funeral of Gore's father, screaming vulgarities at Gore and telling him, "your dad's in Hell".