When he was eight years old his father was executed at Tyburn (2nd June, 1537) for having taken a leading part in the Pilgrimage of Grace. Thomas and his brother Henry were then removed from their mother's keeping and entrusted to that of Sir Thomas Tempest.
In 1549, when Thomas Percy came of age, an Act was passed ‘for the restitution in blood of Mr. Thomas Percy’. Shortly afterwards, he was knighted, and, three years later, in Queen Mary's reign, he regained his ancestral honours and lands. Declared governor of Prudhoe Castle, he besieged and took Scarborough Castle, which had been seized by rebels in 1557. In reward, the Earldom of Northumberland together with the Baronies of Percy, Poynings, Lucy, Bryan, and Fitzpane, were restored to him. He was installed at Whitehall with great pomp, and soon after was named Warden General of the Marches, in which capacity he fought and defeated the Scots. In 1558 he married Anne Somerset, daughter of the Earl of Worcester, who subsequently suffered much for the Faith.
On Elizabeth's accession the Earl, whose steadfast loyalty to the Catholic faith was known, was kept in the North while the anti-Catholic measures of Elizabeth's first Parliament were passed. Elizabeth continued to show him favour, and in 1563 gave him the Order of the Garter. He had then resigned the wardenship and was living in the South. But the systematic persecution of the Catholics rendered their position most difficult, and in the autumn of 1569 the Catholic gentry in the North, stirred up by rumours of the approaching excommunication of Elizabeth, were planning to liberate Mary, Queen of Scots, and obtaining liberty of worship. Thomas, with the Earl of Westmoreland, wrote to the Pope asking for advice, but before their letter reached Rome, circumstances hurried them into action against their better judgment. After a brief success the rising failed, and Thomas fled to Scotland, where he was captured and, after three years, sold to the English Government. He was conducted to York and beheaded, refusing to save his life by abandoning his religion. He was beatified by Leo XIII on 13th May, 1895, and his festival was appointed to be observed in the Dioceses of Hexham and Newcastle on 14th November. His daughter, Lady Mary, founded the English Benedictine Monastery at Brussels from which nearly all the existing houses of Benedictine nuns in England are descended.