At a cocktail party one evening, as related by Lionel Van Deerlin, an oilman from Texas said, "I like the cut of your jib, young fella." He continued, "If you do go into politics, I'd like to help. Here's a check for five thousand dollars. Cash it whenever you decide to run." A few months later, Burgener ran for a city council vacancy, but returned the check, writing, "Thank you very much, but I feel it would be improper to accept so large an amount from a single out-of-state contributor." Burgener was elected to the San Diego City Council in 1953, serving until 1957. On the city council he pushed for the development of Mission Bay Park. Burgener later recalled the office as "the job I enjoyed the least". Burgener was then elected to the California State Assembly 1963–1967 and California State Senate, 1967–1973. Burgener later said his time in the State Capitol constituted his most productive and rewarding years. He was most proud of state legislation he pushed through in 1963 that mandated classroom training for the intellectually disabled. Burgener was elected to five terms in the U.S. House of Representatives, from 1973 to 1983. He had a mostly conservative voting record, but often crossed party lines to work with Van Deerlin, a Democrat, to further San Diego interests. In 1980, Ku Klux Klan leader Tom Metzger won the Democratic primary in Burgener's district, at that time the most populous Congressional district in the country. The Democrats, from Gov. Jerry Brown on down, disavowed Metzger and endorsed Burgener, clinching his election to a fifth term. Burgener dug up and publicized Metzger's frequent, ill-conceived statements and won the election with 86% of the vote, breaking a 40-year-old record for votes received in a House race. In 1982 he did not seek reelection and retired.
Post-political life
Burgener remained active in civic and political affairs after his retirement. He was a Regent of the University of California during 1988–1997. After Burgener's son Rod was diagnosed as developmentally disabled, Burgener became a champion of mentally-disabled children. He has done much work for, and has headed various associations and committees helping retarded children, including the Clair Burgener Foundation for the Developmentally Disabled. After his retirement, Congressman Burgener lived at Rancho Santa Fe, California with his wife Marvia when he was diagnosed with Alzheimer's disease. Burgener died in 2006 in Encinitas, California. He and his wife were survived by two sons, John and Greg.