Mallory was the son of William Mallory and his wife Dorothy Bellingham daughter of Sir James Bellingham of Levens, in Westmorland. John resided at Studley Royal, home to the family since 1452, which was added to their Hutton Conyers estate. 
In November 1640, Mallory was elected together with his father as Member of Parliament for Ripon in the Long Parliament. He was knighted by King Charles in December 1641 and was disabled from sitting in parliament in on 16 January 1642. By August 1642 Mallory had command of a regiment of foot in the King's army. He was governor of Skipton Castle. He later compounded for the delinquency of himself and his father.
Mallory married Mary Moseley, daughter of John Moseley Lord Mayor of York.
- The Tourist's guide: being a concise history and description of Ripon
- MALLORY, Sir John http://www.historyofparliamentonline.org/volume/1604-1629/member/mallory-sir-john-15556-1619. Retrieved 5 June 2015. Missing or empty
- Willis, Browne (1750). Notitia Parliamentaria, Part II: A Series or Lists of the Representatives in the several Parliaments held from the Reformation 1541, to the Restoration 1660 ... London. pp. 229–239.
- Knights of England
- The parliamentary or constitutional history of England. Volume 9
- P. R. Newman The old service: Royalist regimental colonels and the Civil War, 1642-46
|Parliament of England|
Sir Paul Neille
|Member of Parliament for Ripon
With: William Mallory
Sir Charles Egerton