In 1639 trouble was brewing between King and Parliament. Charles I visited Hull to inspect the town's defences, and arsenal - at that time England's largest. He was warmly welcomed and entertained, possibly in what is Wilberforce House today. In 1640 Sir John Hotham was made town Governor and given a strong military detachment to help him. By 1642 the dispute between King and Parliament reached breaking point. With conflict inevitable, Charles tried to change the Governor. He wanted the Earl of Newcastle to take over, but Parliament re-affirmed Hotham as Governor. The King moved his Court to York to be nearer to Hull. The two towns counter-balanced each other - York for the King, Hull for Parliament. On 22nd April the King sent his young son, the Duke of York (later James 11) to Hull. He was entertained by the mayor (Henry Barnard) and Hotham and stayed overnight. Hotham suspected a trap however, and when he heard that the King was also coming he ordered the town gates to be closed and went out on the wall near Beverley Gate to refuse the King entry. Despite the King's alternate threats and bargains Hotham maintained his refusal, even though the mayor was in favour of allowing the King to enter. Charles went back as far as Beverley and the Duke of York was allowed to follow.

    This was the first overt act of the Civil War and Hotham was declared a traitor the next day. The town was besieged for three weeks in July. but the defenders came out of the town twice to attack the royalists, and in their second sally they succeeded in pushing the royalists our of their headquarters at Anlaby. four miles from the town, and the siege was lifted. Hotham's son, John. took a party of troops from Hull and captured Cawood Castle near Selby, thus protecting the town from the west.
However, the Hothams fared no better than had Sir Robert Constable a century earlier, except they probably met a quicker death. In 1643 their enthusiasm for the parliamentary cause had diminished to the point where they began to have talks with the royalist side. On 29th June they were arrested, although Sir John Hotham had escaped as far as Beverley. They were both executed by Parliament in London in 1644. The new mayor, Thomas Raikes, five aldermen (including Henry Barnard) and the vicar of Holy Trinity, formed a defence committee for the own with the mayor as Acting Governor. By this time the whole of Yorkshire, apart from the Hull area was in Royalist hands and early in June 1643 Lord Fairfax, the Parliamentary Commander for the County took refuge in Hull. He was subsequently made Governor.

    The inevitable second siege of the town was started by the Earl of Newcastle (Charles' nominee for Governor in 1642) on 2nd September 1643, using a large army. The defenders destroyed the Charterhouse, which was outside the walls, and used the ruins as a gun emplacement. The first part of the siege was marked by an artillery battle, the royalists firing red hot shot into the town to start fires. Fairtax cut the banks of the River Humber to flood the countryside and impede the royalists on 14th September. Oliver Cromwell brought Parliamentary reinforcements on 261h September, with more troops being brought later by Sir John Meldrum. On 11th October Fairfax took the initiative using his now strong forces to advance out of the town, and after bitter fighting, the Parliamentary Troops over-ran the royalists. The siege ended the next day, and for some years 11th October was a day of thanksgiving in Hull (in later years 11th October became the official day for the start of the famous Hull Fair, although that policy was discontinued in mid twentieth century).

    Because of Hull's resistance the royalists could not take full advantage of their success in the rest of the north, and Fairfax used the town as a base for military operations for the rest of 1643. Hull remained politically quite happy under parliamentary government. Andrew Marvell, one of the town's M.P's was a notable Puritan poet. The one serious royalist plot in the town was in 1657-8, led by Sir Henry Slingsby. This attempt to subvert officers of the garrison was denounced by the officers themselves and Slingsby was executed. The accession of Oliver Cromwell's son, Richard. as Lord Protector of England was well received in the town. However, in 1659 Robert Overton was appointed Governor, a man who had been very unpopular when he had been Deputy Governor in 164S-1655. This probably did not help the cause of the regime in Hull.