In May 1640 he succeeded his father as Lord Fairfax, but being a Scottish peer he sat in the English House of Commons as one of the representatives of Yorkshire during the Long Parliament from 1640 until his death.

He was driven from York, where he was besieging the Royalists, to Selby; then in 1643 to Leeds; and after beating off an attack at that place he was totally defeated on 30 June 1643 at the Battle of Adwalton Moor.

He escaped to Hull, which he successfully defended against Newcastle from 2 September until 11 October 1643, and by means of a brilliant sally caused the siege to be raised.

Fairfax was victorious at Selby on 11 April 1644, and joining the Scots, besieged York, after which he was present at the Battle of Marston Moor (2 July 1644), where he commanded the infantry and was routed.

[2] Fairfax resigned his command on the passing of the Self-denying Ordinance, but remained a member of the Committee for the Government of Yorkshire and was appointed, on 24 July 1645, steward of the manor of Pontefract.

He died from an accident which caused gangrene in his foot[3] on 14 March 1648 and was buried at All Saints' Church, Bolton Percy, in Yorkshire.

[1] He married his second wife, Rhoda Chapman, widow of Thomas Hussey, in October 1646: they had one child, a daughter Ursula.