Pontefract Castle became the property of Thomas, Earl of Lancaster due to his marriage to Alice de Lacy, the daughter of Henry de Lacy. This was at the time when King Edward II was opposed by the barons because of the his obsession with his favourite Piers Gaveston. In 1312 Gaveston was executed by the barons and Lancaster soon afterwards effectively ruled England. At the Battle of Boroughbridge Lancaster was defeated and captured by Edward's army and taken back to Pontefract Castle and executed outside its walls. In 1362, John of Gaunt the son of King Edward III became the Earl of Lancaster due to his marriage a few years earlier to Blanche of Lancaster and became the owner of Pontefract Castle. In 1400 Pontefract Castle was the prison for King Richard II and is thought to be where he was murdered. In 1536, during the reign of King Henry VIII, the castle became the base for an uprising known as the Pilgrimage of Grace. The rebels were unhappy with the King's religious interference.
The castle's final important moment in history came during English Civil wars when it was captured by Parliamentarian troops and orders were given to destroy it.