During the last half of the next century the castle was one of the main strongholds for the House of Lancaster in the War of the Roses and many battles were fought in the surrounding lands. During this time Richard III granted a Royal charter that gave Pontefract many new rights. This did not help him as he lost to Henry VII at Boswell and Henry united the country by marrying Richard's niece. Their son Henry VIII was in his turn crowned and Pontefract became the headquarters for the defence of the realm in the north and once again a home for Kings.
On one visit to Pontefract with Henry VIII, his Queen, Catherine Howard, was unfaithful to him with one of his courtiers and after due trial both she and her lover were executed.