He left Ireland when he was eleven years old, travelling to America with a priest and a trusted family friend who was also his tutor.

Johnston's career with Native Americans started as a wagoner for General Anthony Wayne's Legion of the United States.

Johnston was responsible to the territorial governor, William Henry Harrison, and to the Superintendent of Indian Trade.

He was at this agency during the War of 1812, and organized a Shawnee party under Captain Logan to rescue women and children during the Siege of Fort Wayne, where his brother, Stephen, was killed.

John and Rachel Johnston were married for 38 years before his wife died on 24 July 1840, after eleven days of illness.

The bereavement after the death of his wife in the family home, caused him to leave and move to Cincinnati with a daughter, and then later to Dayton, where he died in 1861 at the age of 86.