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.
Fairfax married Hon. Anne de Vere, daughter of Horace Vere, 1st Baron Vere of Tilbury and Mary Tracy, on 20 June 1637. They had a daughter, Hon. Mary Fairfax (b. 30 July 1638 – d. 20 October 1704), who married George Villiers, 2nd Duke of Buckingham.
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.
When the civil war broke out in 1642, his father, Lord Fairfax, was appointed general of the Parliamentary forces in the north, and Sir Thomas was made lieutenant-general of the horse under him. Both father and son distinguished themselves in the campaigns in Yorkshire.
Sometimes severely defeated, but more often successful, and always energetic, prudent and resourceful, they contrived to keep up the struggle until the crisis of 1644, when York was held by the Marquess of Newcastle against the combined forces of the English Parliamentarians and the Scots, and Prince Rupert hastened with all available forces to its relief. A gathering of eager national forces within a few square miles of ground naturally led to a battle, and Marston Moor (2 July 1644) proved decisive for the struggle in the north. The younger Fairfax bore himself with the greatest gallantry in the battle and, though severely wounded, managed to join Oliver Cromwell and the victorious cavalry on the other wing. One of his brothers, Colonel Charles Fairfax, was killed in the action. But the Marquess of Newcastle fled the kingdom, and the Royalists abandoned all hope of retrieving their affairs. The city of York was taken, and nearly the whole of the north submitted to the Parliament.
Fairfax arrived in London on 12 November 1645. In his progress towards the capital he was accompanied by applauding crowds. Complimentary speeches and thanks were presented to him by both houses of parliament, along with a jewel of great value set with diamonds, and a sum of money. The king had returned from Wales and established himself at Oxford, where there was a strong garrison but, ever vacillating, he withdrew secretly, and proceeded to Newark to throw himself into the arms of the Scots Covenanter army there. Oxford capitulated in June 1646 following the final siege, and by the end of September 1646 Charles had neither army nor garrison in England, following the surrender of Thomas Blagge at Wallingford Castle after a siege conducted by Fairfax. In January 1647 the King was delivered up by the Covenanters to the commissioners of England's parliament. Fairfax met the king beyond Nottingham, and accompanied him during the journey to Holdenby, treating him with the utmost consideration in every way. "The general", said Charles, "is a man of honour, and keeps his word which he had pledged to me."
John Milton, in a sonnet written during the siege of Colchester, called upon the Lord General to settle the kingdom, but the crisis was now at hand. Fairfax was in agreement with Cromwell and the army Leaders in demanding the punishment of Charles, and he was still the effective head of the army. He approved, if he did not take an active part in, Pride's Purge (6 December 1648), but on the last and gravest of the questions at issue he set himself in deliberate and open opposition to the policy of the officers. He was placed at the head of the judges who were to try the King, and attended the preliminary sitting of the court. Then, convinced at last that the King's death was intended, he refused to act. Fairfax had never desired the death of the King. In calling over the court, when the crier pronounced the name of Fairfax, it is said that his wife, Anne Fairfax, said "he had more wit than to be there". Later when the court said that they were acting for "all the good people of England", she shouted ‘No, nor the hundredth part of them!". This resulted in an investigation and Anne was asked or required to leave the court. It was said that Anne could not forbear, as Bulstrode Whitelocke says, to exclaim aloud against the proceedings of the High Court of Justice. In February 1649 Fairfax was elected Member of Parliament for Cirencester in the Rump Parliament. Anne was later approached to intercede on the King's behalf to prevent his execution.
Fairfax's last Service as Commander-in-chief was the suppression of the Leveller mutiny at Burford in May 1649. He had given his adhesion to the new order of things, and had been reappointed Lord General, but he merely administered the affairs of the army; when in 1650 Scots Covenanter Kirk Party eventually declared for Charles II, and the Council of State resolved to send an army to Scotland in order to prevent an invasion of England, Fairfax resigned his commission. Cromwell desired to see him continue as Commander-in-chief, as did those planning the war, but Fairfax could not support the war. Cromwell was appointed his successor, "Captain-general and Commander-in-chief of all the forces raised or to be raised at authority of Parliament within the Commonwealth of England."
In 1654 Fairfax was elected MP for the newly created constituency of West Riding in the First Protectorate Parliament. He received a pension of £5,000 a year, and lived in retirement at his Yorkshire home of Nunappleton until after the death of the Lord Protector in 1658. Nunappleton and Fairfax's retirement there are the subject of Andrew Marvell's country house poem, Upon Appleton House. The troubles of the later Commonwealth recalled Lord Fairfax to political activity, and in 1659 he was elected MP for Yorkshire in the Third Protectorate Parliament. For the last time his appearance in arms helped to shape the Future of the country, when George Monck invited him to assist in the operations about to be undertaken against John Lambert's army. In December 1659 he appeared at the head of a body of Yorkshire gentlemen, and such was the influence of Fairfax's name and reputation that 1,200 horse quit Lambert's colours and joined him. This was speedily followed by the breaking up of all Lambert's forces, and that day secured the restoration of the monarchy. For these actions, along with his honourable conduct in the civil war, he was spared from the wave of Royalist retributions. In April 1660 Fairfax was re-elected MP for Yorkshire in the Convention Parliament. He was put at the head of the commission appointed by the House of Commons to wait upon Charles II, at the Hague and urge his speedy return. Fairfax provided the horse on which Charles rode at his coronation.
The remaining eleven years of the life of Lord Fairfax were spent in retirement at his seat in Yorkshire. His wife died in 1665 and Fairfax died at Nunappleton in 1671. He was buried at Bilbrough, near York.
Fairfax, played by actor Dougray Scott, is a pivotal character in the 2003 Film To Kill a King, as well as in Rosemary Sutcliff's 1953 historical fiction Simon, being portrayed as inspiring and fair. He also appears as a central character in Sutcliff's 1959 novel The Rider of the White Horse, which gives an account of the early stage of the Civil War from the point of view of his wife, and in Howard Brenton's 2012 play 55 Days. Douglas Wilmer portrayed him in the 1970 Ken Hughes film Cromwell. He appears in Michael Arnold's novel Marston Moor, which includes an account of Fairfax's adventures in the eponymous battle. He was also a central character, played by Nigel Anthony, in the 1988 BBC Radio production of Don Taylor's play God's Revolution.
Fairfax had a taste for literature. He translated some of the Psalms, and wrote poems on solitude, the Christian warfare, the shortness of life, etc. During the last year or two of his life he wrote two Memorials which have been published – one on the northern actions in which he was engaged in 1642–44, and the other on some events in his tenure of the chief command. At York and at Oxford he endeavoured to save the libraries from pillage, and he enriched the Bodleian with some valuable manuscripts. His correspondence were edited by G.W. Johnson and published in 1848–49 in four volumes.
With the collapse of the Royalist cause came a confused period of negotiations between the Parliament and the King, between the King and the Scots, and between the Presbyterians and the Independents in and out of Parliament. In these negotiations the New Model Army soon began to take a most active part. The Lord General was placed in the unpleasant position of intermediary between his own officers and Parliament. To the grievances, usual in armies of that time, concerning arrears of pay and indemnity for acts committed on duty, there was quickly added the political propaganda of the Independents, and in July the person of the King was seized by Cornet Joyce, a subaltern of cavalry — an act which sufficiently demonstrated the hopelessness of controlling the army by its articles of war. It had, in fact, become the most formidable political party in the realm, and pressed straight on to the overthrow of Parliament and the punishment of Charles.