With the civil dissensions that came under Henry VI., the castle became again of importance. The Duke of Exeter, taken from sanctuary after St. Alban’s, was here imprisoned; and in 1460, after the battle of Wakefield, Edward here took post, with his army encamped around. It was under the walls of the castle that Warwick killed his horse before the soldiers, saying, “Let him flee that flee will; I stay by him who stays by me.” It was in accordance with this declaration that the king advanced from Pontefract next day, and defeated the Lancastrians at Towton. Edward’s father, Richard, Duke of York, and his brother, the Earl of Rutland, slain at Wakefield, had been buried at Pontefract. He now added his father’s head to his body, and removed the whole from St. John’s Church to Fotheringay. During Edward’s reverses and absence in Holland, the Lancastrians used Pontefract as a military prison.

In 1463, Edward was again at Pontefract, and in 1478, when he was escorted thither in great state, and remained a week.

The bloody celebrity of Pontefract was increased during the ascendancy of Richard, Duke of Gloucester, who sent hither Rivers, Grey, Vaughan, and Hawse, to be executed without form of trial. Soon after his accession he erected the town into a municipal borough.

The castle rose again briefly into notice in 1536, when Aske and the insurgents of the Pilgrimage of Grace appeared before it, and forced its surrender by Lord Darcy and the Archbishop of York, with more than a presumption of treachery. Henry VIII. was here in 1540. Two years later, Sir Henry Savile, as governor, had charge of several Scottish prisoners taken at Solway Moss.

Elizabeth, towards the close of her reign, repaired the castle, and rebuilt the chapel of St. Clement within it. King James was here in 1603, and made the castle and honour a part of the dower of his queen. He repeated his visit in 1616, and viewed the newly-established college of St. Clement, within the castle. King Charles was here in 1625, soon after his accession.

Pontefract was once more to become a place of military importance. Once the centre of the baronage of the north, it was now to appear as the rallying-place of the great aristocracy of Yorkshire, and of the Royal party. In 1642, when Charles lifted his standard at York, Pontefract Castle was garrisoned by a very strong force of local gentry and volunteers, with the gallant Sir William Lowther, of Swillington, as governor. Their courage was soon to be tried. After Marston Moor and the surrender of York, Sir T. Fairfax appeared before the castle, and in December, 1644, commenced its siege. The main attack seems to have been directed upon the north-west angle, where the Pix Tower was battered, and fell, bringing down part of the adjacent curtain with it. The enemy, however, did not storm, and the breach was made good with earth. Mines were then tried, and one was sprung near the King’s Tower, at the south-east angle. These were met by counter mines, for which the ground, a soft rock, was very favourable. Very many shafts were sunk near the walls in the main ward, and, no doubt, are still in existence. Both attack and defence were carried on with great spirit, but at last stores began to fail, and matters looked ill for the garrison. They were reduced to extremity when, on the 1st of March, Sir M. Langdale arrived with 2,000 men from Oxford, and forced Lambert to raise the siege, while he victualled and reinforced the garrison.

The Parliament, however, was now in the ascendant, and in a few days their forces were recruited, and again appeared before the place.

This time regular trenches were opened, batteries thrown up, and a complete line of circumvallation laid out. This was of an oval figure, completely inclosing the castle and its outworks. The contained area, from the head of Micklegate by Knollys’s Hospital on the west, to Monk-hill near New Hall on the east, was 900 yards; and from Baghill on the south, to the middle of the Abbot’s Closes on the north, 700 yards, and about 3,000 yards in girth. Upon this line, which in parts commanded the castle, were thrown up twelve regular places of arms, redans, or batteries, besides flèches and lighter works on the intermediate curtains to beat off the frequent sallies of the garrison. General Sands commanded, and General Overton was governor of the town. New Hall, a large mansion of the Talbots, to the east of the castle and outside the lines, was entrenched, and occupied by Sir John Savile. The garrison held Swillington Tower, the tower of the great church, and Neville’s Mount, a cavalier thrown up by them within the barbican, and carrying a large iron gun. These advanced works were of great service, as they both retarded the siege works and protected the repeated sallies from the garrison.

The trenches were opened in March, but it was the 24th of May before a battery was opened upon the keep. General Poyntz then took the command of the attack. It was, however, late in May before the church-tower was battered down, and the post, therefore, abandoned. Notwithstanding the disastrous news of Naseby, Lowther continued to hold out, and it was not until July 20th, after four months of siege, without further supply of stores or ammunition, and without a chance of relief, that he surrendered upon excellent terms. The fall of Pontefract was followed in three days by that of Sandal Castle, within signal of its towers.

The Parliament spared Pontefract on account of its strength, and put in General Cottrell, with a garrison. The Royalists, however, were still strong in the district, and June 6th, 1648, it was recovered by the treason of Morrice, a renegade, but a man of courage. A garrison was quickly collected, and the castle became once more a Royalist centre.