In 1896, Baker joined the staff of McClure's, a pioneer muckraking magazine, and quickly rose to prominence along with Lincoln Steffens and Ida Tarbell. He also dabbled in fiction, writing children's stories for the magazine Youth's Companion and a nine-volume series titled "Adventures in Contentment" under the pseudonym David Grayson.
In 1906, Baker, Steffens and Tarbell left McClure's and created American Magazine. In 1908, he wrote the book Following the Color Line, becoming the first prominent journalist to examine America's racial divide. He would continue that work with numerous articles in the following decade.
In 1912, Baker supported the presidential candidacy of Woodrow Wilson, which led to a close relationship between the two men, and in 1918 Wilson sent Baker to Europe to study the war situation. During peace negotiations, Baker served as Wilson's press secretary at Versailles. He eventually published 15 volumes about Wilson and internationalism, including an 8-volume biography, the last two volumes of which won the Pulitzer Prize for biography in 1940.
Baker died in Amherst, Massachusetts of a heart attack.