Johnson was born on January 1, 1774, in Orange County, Virginia. When he was six years of age, his father, Robert, and his mother, Jemima (Suggett) Johnson, migrated to Pennsylvania, where they remained one year before they moved to Kentucky and settled ultimately at Great Crossings, or Bryant's Station, near Lexington.
In 1782 Bryant's Station was attacked by a large body of hostile Indians. The supply of water in the fort became exhausted and the women went to the spring for more, thinking that the Indians would be less likely to fire upon them than upon the men. It was Jemima Johnson who volunteered to lead the party and she accomplished the feat unmolested. Her husband also established his reputation in the new country. He acquired the title of colonel, was appointed in 1796 on the commission to determine the boundary between Kentucky and Virginia, and sat in the first and second constitutional conventions of his state.