General James Johnston is buried in the centre part of the nave of Westminster Abbey. Only a small stone now marks his grave, near that of Thomas Telford. Many of the gravestones in the nave were taken up in 1834 as the floor was damaged. The inscription on his original stone read:
Here lie the mortal remains of James Johnston an old soldier and faithfull subject who began his military career as a Cornet on the 1st day of October 1736 and finished it as a General of His Majesty's Forces, Governor of the town of Quebeck in the province of Canada, and Colonel of the 6th or Enniskillen Regiment of Dragoons on the 13th of December 1797 which day he departed this life at his house at Hampton in the county of Middlesex in the 77 year of his age.
He was the only surviving son of Captain George Johnston, descended from the family of that name in Hilton in what was the county of Berwickshire, and his wife Hester (Bland). George became an army agent in Dublin and Hester was a daughter of the Dean of Ardfert in Ireland. James married on 5th May 1763 Lady Henrietta West (d.1817), daughter of John, Earl Delawarr. His son Henry's wife Jane, and his daughter Caroline, wife of Evelyn Anderson, were mentioned in his will, as was his sister Margaret and children of his sister Mary, Lady Napier.