In 1821 when Johnson was seven, his parents moved the family to Arkansas Territory, where his father had been appointed as Superior Judge. They settled in Little Rock. His father was appointed in 1836 as the first federal district judge in the new state of Arkansas. Johnson was later sent back to Kentucky to study at the Choctaw Academy, which his uncle Richard Johnson had founded in 1825 on his farm near Georgetown, primarily to educate Choctaw boys from the Southeast in the English language and European-American culture. He was handsomely paid by the federal government.