He moved west and taught school in St. Louis, Missouri, from 1857 to 1880, where he was superintendent of schools from 1868 to 1880, and established, with Susan E. Blow, America's first permanent public kindergarten in 1873. It was in St. Louis where William Torrey Harris instituted many influential ideas to solidify both the structural institution of the public school system and the basic philosophical principles of education. His changes led to the expansion of the public school curriculum to make the high school an essential institution to the individual and to include art, music, scientific and manual studies, and was also largely responsible for encouraging all public schools to acquire a library.
Harris's St. Louis Schools were considered some of the best in the country. His fellow educators were local farmers that immigrated from Germany after they tried and failed to make Germany a republic.
He was a key member of a philosophical society that, during the beginning of the American Civil War, met in St. Louis; it promoted the view that the entire unfolding was part of a universal plan, a working out of an eternal historical dialectic, as theorized by Hegel.
Harris was associated with Bronson Alcott's Concord School of Philosophy from 1880 to 1889, when he became U.S. Commissioner of Education, serving until 1906. He did his best to organize all phases of education on the principles of philosophical pedagogy as espoused by Hegel, Kant, Fichte, Fröbel, Pestalozzi and many others of idealist philosophies. He received the degree of LL.D. from various American and foreign universities.
As the United States Commissioner of Education, Harris nearly succeeded in making Hegelianism the official philosophy of American education during the late 19th century.
He was also assistant editor of Johnson’s New Universal Cyclopaedia and editor of Appletons' International Education Series. He expanded the Bureau of Education and started graphic exhibits of the United States in international expositions.
In 1906 the Carnegie Foundation for the Advancement of Teaching conferred upon him "as the first man to whom such recognition for meritorious service is given, the highest retiring allowance which our rules will allow, an annual income of $3000."
- He was responsible for introducing reindeer into Alaska so that the native whalers and trappers would have another livelihood, before they brought other species to extinction.
- Harris was one of the 30 founding members of the Simplified Spelling Board, founded in 1906 by Andrew Carnegie to make English easier to learn and understand through changes in the orthography of the English language.