He was eldest son of John Johnston (d. 1657), by Elizabeth, daughter of Henry Hobson of Usflete, Yorkshire.
[1] Ralph Thoresby first made Johnston's acquaintance at Pontefract on 26 February 1682, and became a great friend and a correspondent.
He largely followed Hobbes, and, besides much classical learning, shows considerable knowledge of English chroniclers and legal authorities.
In 1687, in answer to a pamphlet of Sir William Coventry, he issued The Assurance of Abby and other Church Lands in England, the object of which is to demonstrate that even if the religious orders were restored in England, the possessors of the church lands confiscated by Henry VIII could not be disturbed.
In the same year he published a volume of political Enquiries, and subsequently The Dear Bargain … the State of the English Nation under the Dutch, anon.
[1] For thirty years Johnston studied the antiquities of Yorkshire, and he left over a hundred volumes of collections, written in a very crabbed hand.
He intended writing volumes on the model of William Dugdale's Warwickshire and Robert Plot's Natural History of Staffordshire.
On Henry Johnston's death in 1755, ninety-seven volumes were purchased by Richard Frank of Campsall, Yorkshire, who allowed John Burton, to examine them when preparing his Monasticon Eboracense.