In 1622 he was made a baronet, and he was member of parliament for Beverley in the five parliaments between 1625 and 1640, being sheriff of Yorkshire in 1635. In 1639 he was deprived by the king of his office of governor of Hull, and joiqing the parliamentary party refused to pay ship-money. In January 1642 Hotham was ordered by the parliament to seize Hull, where there was a large store of munitions of war; this was at once carried out by his son John. Hotham took command of Hull and in April 1642 refused to admit Charles I to the town. Later he promised his prisoner, Lord Digby, that he would surrender it to the king, but when Charles appeared again he refused a second time and drove away the besiegers.
Meanwhile the younger Hotham was taking an active part in the Civil War in Yorkshire and Lincolnshire, but was soon at variance with other parliamentary leaders, especially with the Fairfaxes, and complaints about his conduct and that of his troops were made by Cromwell and by Colonel Hutchinson. Soon both the Hothams were corresponding with the earl of Newcastle, and the younger one was probably ready to betray Hull; these proceedings became known to the parliament, and in June 1643 father and son were captured and taken to London.
After a long delay they were tried by court-martial, were found guilty and were sentenced to death. The younger Hotham was beheaded on the 2nd of January 1645, and in spite of efforts made by the House of Lords and the Presbyterians to save him, the elder suffered the same fate on the following day. Sir John Hotham had two other sons who were persons of some note: