Johnson was born near Amsterdam, New York on 5 November 1741. He was the only son of Colonel Sir William Johnson, 1st Baronet, and his common-law wife, Catherine Weissenberg, a Palatine German immigrant. As his parents never married, he was baptized John Wysen Bergh by Rev. Henry Barclay February 7, 1741/2 as an Anglican in the chapel at Fort Hunter. His father was a military commander during the French and Indian War (Seven Years' War) who had promoted the British settlement of the Mohawk Valley and trading with the Mohawk, and founded the community of Johnstown in Tryon County in the Province of New York.