Young graduated from the Chicago Normal School in 1862 and taught primary school before becoming principal of the new practice school of the Chicago Normal School (1865–71). She taught high school from 1871 to 1875 and was principal of a grammar school from 1875 to 1877. In 1887 she was appointed assistant superintendent of Chicago schools, a position she held for 12 years.

In 1895 Young began studying part-time under John Dewey (Dewey, John) at the University of Chicago, and on her resignation as assistant superintendent in 1899, she was appointed associate professor of pedagogy at the University of Chicago. She received a Ph.D. (1900) and was then advanced to full professor. Her dissertation, published as Isolation in the School (1900), was the first of the three volumes Young wrote for the University of Chicago series entitled Contributions to Education. The other two titles are Ethics in the School (1902) and Some Types of Modern Educational Theory (1902).

In 1905 Young became principal of the Chicago Normal School (a second school of that name, later Chicago Teachers College, now Chicago State University). In 1909 she was appointed superintendent of Chicago schools, becoming the first woman to head the school system of a major city in the United States. Improvement in teacher training, recognition of teaching as a profession, and broadening of teacher responsibilities were the major policy goals of Young's office. She also included vocational and physical training in school curricula. In 1910, aided by Margaret Haley (Haley, Margaret Angela), Young was elected the first woman president of the National Education Association.

In 1913 Young resigned as superintendent. After much controversy and a public protest led by Jane Addams and others, Young was reappointed; however, she resigned permanently in 1915.