His first military experience came during the Thirty Years War, serving in the Netherlands (1629-31), and taking part in the siege of Bois-le-Duc (1629). He held a command during the First Bishops War (1639), and despite the lack of any fighting was knighted the following year. Immediately before the outbreak of the Civil War, he and his father, Ferdinando Fairfax, were amongst the most important supporters of Parliament in Yorkshire, even confronting Charles I with a petition on 3 June at what had been intended as a royalist rally, and once war was declared became one of the key Parliamentary generals in Yorkshire. However, his first encounter was a defeat at Tadcaster (7 December 1642), after which he was forced to retreat, while the Royalists occupied the West Riding of Yorkshire, which with it's puritanical mill towns had been a key part of Parliaments plans for Yorkshire. However, the situation soon improved, and with the aid of a large number of men from Halifax, Fairfax was able to capture Leeds (25 January 1643). In April he was once again surprised by a Royalist force, under George Goring, on Seacroft Moor, forcing him back to Leeds. Under pressure from the relatives of prisoners captured at Seacroft Moor, he launched a raid on Wakefield, with the intention of taking Royalist prisoners. The attack, on 20 May 1643, was more successful than he had expected, and Goring was himself captured, although the town was abandoned, and Fairfax withdrew to Bradford. Emboldened by this successes, Fairfax and his father gathered their forces, and marched to Bradford, threatened by the larger, but badly equipped, Royalist army of the Marquis of Newcastle. The two armies clashed on 30 June 1643 at Adwalton Moor, where the 19,000 strong Royalist army defeated the much smaller Parliamentary army. Fairfax managed to break into Bradford despite the royalist siege, to rescue his wife and daughter, but although he escaped with his daughter, his wife was captured. He managed to limp into Hull, fearing for his daughters wife after the journey, but his spirits soon recovered. His daughter quickly recovered, while Newcastle, demonstrating the gallantry common to both sides in the war in Yorkshire sent Fairfax's wife to Hull, in his own carriage, although Newcastle soon resumed the offensive, flooding the area around Hull. Fairfax made his escape from the city by boat, moving his troops to Lincolnshire, where he met up with Oliver Cromwell. Despite Royalist dominance of Yorkshire, Hull still held for Parliament, and during the autumn, both Fairfaxes were in the city. This time Cromwell crossed the Humber, leaving Lord Fairfax as governor of Hull, and taking Thomas back across to Lincolnshire, along with the remnants of his cavalry.
Fairfax now moved closer to the centre of the Parliamentary war effort. In late October 1643, he was present at the battle of Winceby, where Cromwell's Ironsides demonstrated their qualities, and carried the battle even after Cromwell's own horse was shot from under him. January 1644 saw the war enlarged. Parliament gained Scottish aid, in return for promising to protect Presbyterianism in Scotland, and a Scottish army crossed the border, while Charles managed to arrange a temporary peace in Ireland, which allowed him to raise a new army in Ireland, which landed soon threatened Cheshire. The Irish threat was soon dealt with. Fairfax was sent across the Pennines to deal with the new threat in the Welsh Marches, and after a slow journey, reached Cheshire, where the new Royalist army, under Lord Byron, was besieging Nantwich, the only Parliamentary stronghold in the county. Aware of Fairfax's approach, late on 23 January Lord Byron started to reassemble his army, split by the frozen River Weaver. The resulting battle of Nantwich (24 January 1644), was made much easier for Fairfax by a sudden thaw. The river rose, swept away the only bridge in Lord Byron's command, and split his army in two. Fairfax attacked, and with the aid of a sortie from the town, won a resounding victory. The Royalist infantry surrendered almost intact, and then joined the Parliamentary side, while Byron was only able to escape with his cavalry. Fairfax then moved on to besiege Lathom House, but although he started the siege, by the time the first shots had been fired in early March, Fairfax had already been ordered back to Yorkshire. where the Royalist garrison of York were causing problems. After meeting with his father, the two Fairfaxes defeated the temporary governor of York, Colonel John Bellasis, at the battle of Selby (11 April 1644). News of the battle caused both Newcastle with the Royalist army and Leven with the Scottish army to rush back from Durham. Newcastle managed to get into York, where from the end of April he was besieged by the combined forces of Fairfax and Leven, soon joined by the earl of Manchester. Despite their overwhelming numbers, after two months it looked as if their efforts had been in vain. Prince Rupert with a relieving army managed to evade them, and reach the city on 1 July, before turning to face the besiegers the following day.
The resulting battle of Marston Moor (2 July 1644) undid Prince Rupert's good work. However, it was a close run thing. Fairfax had command of the cavalry on the Parliamentary right, which scattered and ran when charged by Lord Goring. Fairfax was one of the few to remain on the field (although his father did run from the field).
Fairfax now had one of the highest reputations amongst Parliamentary generals. When, in the aftermath of the second battle of Newbury, Parliament decided to form the New Model Army, Fairfax was the popular choice to command it, and on 21 January 1645 Parliament made him commander in chief of the new army, with Skippon in charge of the Infantry, and Cromwell as his second in command and commander of Cavalry. By the end of April, the new army was ready to move. Initially, Fairfax was ordered to march towards the west country, but early in May he was ordered to turn around and march towards Oxford. For a brief period, Fairfax was deeply vulnerable, split from Cromwell, and facing potential attack by much larger Royalist forces, but the Royalists missed their chance, and Fairfax settled down to besiege Oxford. For the moment the city was saved, by the capture of Leicester on 30 May, which forced Fairfax north with orders to recapture the city. He soon joined with Cromwell, and the full New Model Army headed towards it's first major battle.
The Battle of Naseby (14 June 1645) was the deciding battle of the war. Although he was commander, Fairfax does not figure greatly in accounts of the battle, the glory going to Cromwell and his cavalry, who did indeed do the most important fighting, but Fairfax appears to have been an active general, seen all along the line. The battle destroyed the heart of the Royalist armies, especially amongst the infantry, which was never to recover. Meanwhile, Fairfaz and the New Model moved on to deal with the King's army in the west, under Goring. This army too was defeated, at the battle of Langport (10 July 1645), where the New Model Army once again showed it's quality. Fairfax and the New Model then moved on to deal with the remaining Royalist strongholds in the south, including Sherborne castle, taken on 14 August, Bristol, taken on 10 September despite the presence of Prince Rupert in the garrison, and Berkeley Castle, taken on 26 September. Fairfax began 1646 by marching into Devon and Cornwall to deal with Hopton and the remnants of the King's Cornish army. After inflicting a defeat on them at Torrington (16 February 1646), Fairfax forced them back to Truro, where on 13 March Hopton surrendered and agreed to go into exile. Finally, at the end of June, the garrison of Oxford surrendered.
For the moment, Fairfax was the hero of the day. On his return to London, he was honoured by a visit from both houses of Parliament (14 November). Fairfax was still commander in chief, and now he faced the task of preparing the army for peacetime. This was made much harder by the Presbyterian majority in Parliament, who now saw the army as a dangerous hotbed of Independent thought, and wished to dismiss it as quickly and cheaply as possible. This rapidly politicised the army, causing Fairfax great personal problems. While he remained General, he did not approve of the army getting involved in politics. This meant that he still retained command when the Second Civil War broke out. Having sent Cromwell to deal with the revolt in the west, Fairfax himself dealt with the rebels in Kent, where the only serious problems he encountered were at Colchester, which held out from 14 July until 28 August.
After this second civil war, the mood turned against the king. Fairfax was one of the judges at the trial of Charles I, he fought to prevent his execution. He finally resigned in 1650 in protest against plans to invade Scotland (Third Civil War), and retired into private life. He only emerged from his retirement in 1659, sitting in Richard Cromwell's parliament. After the collapse of Richard's government, he played a major part in the restoration of Charles II, heading the commission sent to Charles at the Hague, but on his return to England returned to his retirement.