Thomas was the only black person at his high school in Savannah, where he was an honor student.[ He was raised Roman Catholic. (He later attended an Episcopal church with his first wife but returned to the Catholic Church in the late 1990s.) He considered entering the priesthood at the age of 16, and became the first black student to attend St. John Vianney's Minor Seminary (Savannah) on the Isle of Hope.[9] He also briefly attended Conception Seminary College, a Roman Catholic seminary in Missouri. No one in Thomas's family had attended college. Thomas has said that during his first year in seminary, he was one of only "three or four" blacks attending the school. Thomas told interviewers that he left the seminary in the aftermath of the assassination of Martin Luther King, Jr. He had overheard another student say after the shooting, "Good, I hope the son of a bitch died." He did not think the church did enough to combat racism.[9]
At a nun's suggestion, Thomas attended the College of the Holy Cross in Worcester, Massachusetts. While there, Thomas helped found the Black Student Union. Once he walked out after an incident in which black students were punished while white students went undisciplined for committing the same violation, and some of the priests negotiated with the protesting black students to return to school.[10]
Having spoken the Gullah language as a child, Thomas reportedly realized in college that he still sounded unpolished despite having been drilled in grammar at school, and he chose to major in English literature "to conquer the language".[12] At Holy Cross, he was also a member of Alpha Sigma Nu and the Purple Key Society.[13] Among Thomas's classmates at Holy Cross were future defense attorney Ted Wells and author Edward P. Jones, who won the Pulitzer Prize for his novel, The Known World.[14] Thomas graduated from Holy Cross in 1971 with an A.B. cum laude in English Thomas entered Yale Law School, from which he received a Juris Doctor (J.D.) degree in 1974, graduating towards the middle of his class.[16]