Thomas Fairfax was born at Denton Hall, halfway between Ilkley and Otley in the West Riding of Yorkshire, on 17 January 1612, the eldest son of Ferdinando Fairfax, 2nd Lord Fairfax of Cameron (his family title of Lord Fairfax of Cameron was in the peerage of Scotland, then still independent from England, which was why he was able to sit in the English House of Commons after he inherited it). He studied at St John's College, Cambridge, and Gray's Inn (1626–1628), then volunteered to join Sir Horace Vere's expedition to fight for the Protestant cause in the Netherlands.
In 1639 he commanded a troop of Yorkshire dragoons which marched with King Charles I against the Scots in the First Bishops' War, which ended with the Pacification of Berwick before any fighting took place. In the Second Bishops' War the following year, the English army was routed at the Battle of Newburn. Fairfax fled with the rest of the defeated army but was nevertheless knighted in January 1641 for his services.