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In 1818, the Baptist Mission Society of Kentucky started the Choctaw Indian Academy at Great Crossings, Kentucky, located near Georgetown and Johnson’s home. The school soon failed, however, from a lack of funding. When some Choctaw Mississippi lands were ceded to the United States, the tribal leaders requested that some of the treaty money be used to fund educational initiatives. Therefore, they reached out to Johnson. The congressman, along with his brother-in-law, William Ward, the U.S. government agent for the Choctaw Nation in Mississippi, had the school restarted in 1821.

The end of the school had its roots in the Indian Removal Act of 1830. That legislative action led to the migration of thousands of Native Americans to west of the Mississippi River to Indian Territory, now present-day Oklahoma. There, many of the migrating tribes —including the Choctaw—started their own reservation schools and attendance began to dwindle at Johnson's Kentucky school. After the Choctaws eliminated their financial support for the school it soon closed in 1842.


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