In the first Bishops' War Fairfax had commanded a regiment in the king's army; then on the outbreak of the English Civil War in 1642 he became commander of the parliamentary forces in Yorkshire, with Newcastle as his opponent. Hostilities began after the repudiation of a treaty of neutrality entered into by Fairfax with the Royalists. At first Fairfax met with no success. 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. He was subsequently, in July 1644, made Governor of York and charged with the further reduction of the county. In December 1644 he took the town of Pontefract, but failed to secure the castle.