Thompson was elected as a Democrat to the Thirtieth Congress (March 4, 1847 – March 3, 1849); he declined to be a candidate for reelection.
In 1852 he served as a delegate to the Democratic National Convention, and as a member of the board of visitors of his alma mater, the University of Virginia.
Thompson moved to San Francisco, California, in 1853. That same year, he was appointed to a commission to settle private land claims in his adopted state. In 1870, he was appointed by the Governor as a reporter of the California Supreme Court, and also joined the justices' court of San Francisco; he served on that court until his death in San Francisco in 1876.
He was interred in Laurel Hill Cemetery in San Francisco, but upon the dissolution of that cemetery (between 1939 and 1941) he was re-interred at Cypress Lawn Memorial Park in Colma, San Mateo County, California.
Thompson's son, Thomas Larkin Thompson, settled in Sonoma County, north of San Francisco. He was elected to Congress in 1886 from the 1st Congressional District, which then covered much of northern California, but was defeated for re-election in 1888.