In 1828, Thompson was married to Electa Ferris (1808–1902), a daughter of Lydia Smith Ferris and Solomon Ferris. They resided in New York City at 295 Madison Avenue and summered at
The Anchorage in Highland, New York. Together, Electa and John were the parents of six children, including: a son of Herman Culyer Adams, in 1851. • Samuel C. Thompson (1835–1884), who married Abigail E. Sherman (1841–1907), daughter of Edward T Sherman. •
Frederick Ferris Thompson (1836–1899), who married
Mary Lee Clark, daughter of
Governor Myron Holley Clark, in 1857. After a severe illness that lasted four months, Thompson died on April 19, 1891, at his home in New York at 295 Madison Avenue. His wife died at her home in New York in September 1902 at the age of 95. ==References==