The court specially convened in January 1649 to conduct the trial of King Charles I.
The trial of King Charles I was authorised by an ordinance of the House of Commons passed, without the consent of the Lords, on 6 January 1649. A committee headed by Oliver Cromwell, Henry Ireton, Henry Marten and Thomas Scot drew up a list of 135 commissioners to judge the King, consisting mainly of landed gentry, lawyers, aldermen and army officers. Around 70 of those nominated actually attended the trial, with Sir Thomas Fairfax foremost amongst the absentees.
The Chief Justices Henry Rolle and Oliver St John refused to serve on the High Court and most of the lawyers nominated as commissioners also withdrew. Attorney-General Anthony Steele claimed that he was too ill to present the case against the King. Eventually John Bradshaw, a relatively obscure magistrate from Cheshire, was appointed Lord President of the court, and the radical lawyer John Cook appointed chief prosecutor. Cook drew up the charges against the King with legal advice from Isaac Dorislaus.
The King's trial opened on 20 January 1649. He was condemned to death on 27 January with 59 Commissioners signing the death warrant.
In February 1649, the High Court was reconvened for the trial of five Royalist leaders of the Second Civil War, of whom three were sentenced to death: the Duke of Hamilton, the Earl of Holland and Lord Capel.
The High Court of Justice was summoned again in May 1658 following the discovery of a Royalist conspiracy against Cromwell's Protectorate to foment an uprising in England to be synchronised with an invasion by Charles Stuart (Charles II) and a Spanish army. Around 140 magistrates, lawyers, MPs, soldiers and aldermen were appointed as commissioners to judge the ringleaders of the plot, but only around 50 were willing to act, with John Lisle serving as Lord-President. Despite legal arguments that the plotters should be tried by jury, the trials went ahead and a number of ringleaders were executed.