On January 24, 1862, the Territorial Legislature of Washington specified that one of the University of Washington's four original institutional departments would be dedicated to the study of military science. Although the creation of a military department was mandated at the opening of the Civil War, it was not until the late 1870s that plans were developed. Finally, in 1882, the university president established a military department and in 1884, an active program was in place. From 1892 until 1916, with the exception of the period between 1902 and 1909, the Board of Regents adhered to a policy of requiring all male students to participate in military training for the first two years.

In 1916, the responsibilities for military training were transferred to the federal government's newly created Reserve Officers' Training Corps (ROTC). The requirement for two years of compulsory basic ROTC was stated in the 1919-1920 catalog and was continued in successive catalogs until the start of World War II. In 1946, the University removed the compulsory aspect of the military science requirement from the catalog; however two-year compulsory basic ROTC was reinstated at the recommendation of the University Senate and the Board of Deans in 1948. After prolonged study, military programs on campus became entirely voluntary in 1962 and have continued in this status to the present time.

The Kinnear Husky Battalion take its name from Cadet Captain C.A. Kinnear, who led a group of UW cadets during an operation to assist the Seattle City authorities in quelling the Anti-Chinese Riots of 1886. The unit received the title Kinnear Husky Battalion in 1984. For their assistance to local authorities, General John Gibbon presented the Battalion with a silk 38-star American flag in 1987, still on display on the ground floor of Clark Hall, outside the Military Science Department offices.