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 I 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 infantry in the King's army. He was governor of Skipton Castle. He later compounded for the delinquency of himself and his father.