He was the son of Jotham Johnson and Hannah (Crosby) Johnson, and was born in Thompson, Windham County, Connecticut. In November 1826, he removed to Delhi, New York, where he studied law, first with his brother Noadiah Johnson (1795–1839) who was District Attorney of Delaware County from 1827 to 1833, and then with Amasa J. Parker. Stephen was admitted to the bar in 1830, and on January 6, 1831, he married Mary Ann Swift (1808–1886).
