Thomas grew up in Savannah, Georgia, and was educated at the College of the Holy Cross and at Yale Law School. In 1974, he was appointed an Assistant Attorney General in Missouri and subsequently practiced law there in the private sector. In 1979, he became a legislative assistant to Senator John Danforth (R–MO) and in 1981 was appointed Assistant Secretary for Civil Rights at the U.S. Department of Education. In 1982, President Ronald Reagan appointed Thomas Chairman of the Equal Employment Opportunity Commission (EEOC).
In 1975, when Thomas read Race and Economics by economist Thomas Sowell, he found an intellectual foundation for his philosophy. The book criticized social reforms by government and instead argued for individual action to overcome circumstances and adversity. He was also influenced by Ayn Rand, particularly The Fountainhead, and would later require his staffers to watch the 1949 film version. Thomas acknowledges having “some very strong libertarian leanings”.
Thomas returned to the Catholic Church in the mid-1990s.In his 2007 autobiography, he criticized the church for its failure to grapple with racism in the 1960s during the civil rights movement, saying it was not so “adamant about ending racism then as it is about ending abortion now”