Johnson's only novel, The Autobiography of an Ex-Colored Man, was originally published anonymously in 1912. It is a fictional novel written as a memoir of an unnamed biracial narrator who grew up in the South during the Reconstruction and post-Reconstruction eras.

It is a story in which the narrator relates how as a young boy he initially assumed that he was white, and how his notions of racial identity were suddenly turned upside down one day—how from that moment on he was inclined to view himself and the world about him from the perspective of blackness. The novel received very little notoriety until Johnson republished it in 1927, this time taking full credit as its author. - Summary by James K. White