Emerson was born in Trenton, New Jersey to Edwin Emerson, a Professor of Political science,and Mary Louisa (Ingham) Emerson, daughter of Samuel D. Ingham, a U.S. Congressman and U.S. Treasury Secretary under President Andrew Jackson. Emerson attended private schools in Europe, and from 1872 to 1875 studied engineering at the Technical University Munich.
After returning to the United States in 1876, Emerson was appointed as Professor of Modern Languages at the University of Nebraska, where he was dismissed in 1882 because of his progressive educational ideas. In the years after, Harrington had several jobs, including a frontier banker, land speculator, tax agent, troubleshooter, lecturer, and educator. In 1893, he joined William Jennings Bryan's campaign for the presidential election of 1896, which created the foundation for his career as efficiency engineer.
In 1897, Emerson started focusing on mechanical engineering, and was employed shortly after by the Electric Storage Battery Company in New York. After his new projects during the Alaskan Gold Rush failed, he became the general manager in a small glass factory. In 1900, he established the Emerson Institute in New York City in order to focus on his work as efficiency engineer. Through the American Society of Mechanical Engineers, he got acquainted to the work of Frederick W. Taylor, which he implemented in his own praxis.