Johnson is best remembered for his leadership of the National Association for the Advancement of Colored People (NAACP), where he started working in 1917.
In 1920 he was the first black to be chosen as executive secretary of the organization, effectively the operating officer, from 1920 to 1930.
Johnson established his reputation as a writer, and was known during the Harlem Renaissance for his poems, novels, and anthologies collecting both poems and spirituals of black culture.
He was appointed under President Theodore Roosevelt as US consul in Venezuela and Nicaragua for most of the period from 1906 to 1913. In 1934 he was the first African-American professor to be hired at New York University.