William Stanley fought on the Yorkist side at the Battle of Blore Heath in 1459, whereas his elder brother Thomas, Lord Stanley had raised troops by the commission of the Lancastrian Crown but refrained from committing his forces on either side. Attainted in 1459, he fled into exile, but returned to fight for the Yorkists in 1461 at Towton. In 1465 he was granted the Skipton lands and castle of the dispossessed Lancastrian Cliffords. Following the Battle of Tewkesbury in 1471, it was he who captured Queen Margaret of Anjou, who led the Lancastrian faction, and he was made a Knight Banneret by the king. In 1483 he was made Chief Justice of North Wales. Richard III, shortly after becoming king, rewarded Sir William by granting him land in North Wales.