Born in Florida, the son of a Reconstruction politician, Thomas was particularly productive before his thirtieth year, completing such important literature as Black and White: Land, Labor and Politics in the South and The Negro in Politics while in his twenties.

He attended Howard University for two years, leaving to marry Miss Carrie Smiley of Jacksonville, Florida. The couple went to New York in 1878, with Fortune taking a job as a printer for the New York Sun. In time, Thomas caught the attention of Sun editor Charles A. Dana, who eventually promoted him to the editorial staff of the paper.

He also edited The Globe, a black daily, and was later chief editorial writer and polemicist on the staff of The Negro World.

In 1900, Thomas joined Booker T. Washington in helping to organize the successful National Negro Business League. His later activity with Washington gained him more notoriety than his earlier writing, although the latter is clearly more vital in affording him an important niche in the history of black protest.

In 1883,he founded the New York Age, the paper with which he sought to "champion the cause" of his race. In time, the Age became the leading black journal of opinion in the United States. One of his early crusades was against the practice of separate schools for the races in the New York educational system.

Fortune was later responsible for coining the term "Afro-American" as a substitute for Negro in New York newspapers. He also set up the Afro-American Council, an organization which he regarded as the precursor of the Niagara Movement.

In 1907, Fortune sold the Age, although he remained active in journalism as an editorial writer for several black newspapers.

At the time of his death in 1928, Fortune was writing for the Negro World.