District 39, St. Marys, was formed in 1869. A parochial school started in 1881. The frame building was moved from the "hill" to 5th Street in 1887 and a new, stone structure was dedicated in 1893. A transportation system, developed in 1909, consisted of a team and wagon to meet students crossing the river by ferry. Old St. Marys High School was built in 1931 across from the current swimming pool on Lasley Street. The public and parochial schools merged in 1946.

In 1966, St. Marys, Rossville, Emmett and Delia became one district, USD 321, Kaw Valley.

The 1978 bond issue brought about the construction of a new building at 601 E. Lasley, on the old Jesuit college grounds. Students moved to the new building in 1981. The football field was added in 1982 and the track in 1983.

Old St. Marys High School was torn down in 1983, and the shop addition was turned into a senior citizens center. Old hill school was sold to the city in 1982 and razed in 1983.

The first graduating class of St. Marys High was the Class of 1899, thus making the graduates from the Class of 1998 the 100th graduating class.