Columbia City began as an independent milltown in the Rainier Valley. Columbia City School started out in Columbia School District No. 18, which was organized in 1876. A large belltower stood above the main entrance of the two-story building.

When Southeast Seattle became part of the city in 1907, Columbia City School was annexed into the Seattle School District. At this time, its enrollment stood at 514 students in grades 1-8. At the same time, two other smaller schools from Columbia School District, Hillman at 39th Avenue S and Main Street, and Southeast Seattle, at Rainier Avenue and Genesee Street, operated as annexes to Columbia City for a brief time. Hillman closed in 1908, while Southeast Seattle closed in 1909. The Southeast Seattle site was condemned by the Seattle Housing Authority in 1943. The old school bell is located at the Columbia City Historical Society