Second child but first son of Henry Howard, Earl of Surrey, and his wife, Frances Vere. The blow of Surrey's attainder and execution was hardest for Thomas, who was at once separated from his brother, Henry, and his sisters, Jane, Margaret and Catherine. They were taken from their mother's care and placed under the nominal guardianship of Lord Wentworth, though in fact their inmediate custodian was Thomas Gawdy, an old friend of the family. But Thomas Howard was placed with Sir John Williams, Treasurer of the Court of Argumentations. His keeper was kept by busines in London most of the time, while the boy lived quietly at Rycote, the same where Princess Elizabeth spend a similar period of confinement during Mary's reign.

After a difficult year the children were reunited, for the Privy Council decided to place them under the guardianship of their aunt, the Duchess of Richmond, at Reigate Castle. They were joined there by Charles Howard, their cousin, two years older than Thomas, son of Lord William Howard of Effingham. Probably on Lord Wentworth's advice, the Duchess engaged John Foxe as tutor of her charges. Edward VI knew 'no better place for their virtuous education' than with their aunt. At Christmas 1551 the Duchess of Richmond was granted an annuity of £100 towards their maintenance, and the next year was given a further £100.

When Edward died and Mary came to the throne, the Howard fortunes changed. When the Queen rode to London to take up her residence in the Tower until coronation day, the Duchess of Norfolk came with her. Thomas Howard, third Duke of Norfolk was released from his confinement and the Council restored him to the Order of the Garter at their meeting on 10 Aug. Young Thomas soon joined the Duke in London and at the end of the month the Countess of Surrey was ordered by the Council to have the rest of her children brought from Reigate Castle to Mountjoy Place.

Thomas was made Knight of the Bath on Michaelmas Day, the youngest of those created. Next day he rode with his fellows through the city, escorting the Queen to Westminster Abbey for her coronation.

After the Coronation the old Duke decided that his grandosns must be taken in hand, and that the heretic education they had been imbibing for five years must be eradicated. For the moment, Thomas Howard joined the household of Stephen Gardiner as a page. Later, joined with his brother Henry, continued his instruction in the London house of John White, a priest as unbending in his devotion to papal principles as Bonner or Gardiner, and who later become Bishop of Lincoln (Mar 1554) and succeeded Gardiner in the see of Winchester (1556). After a short stay in White's household, Thomas Howard was appointed as one of the seven gentlemen of the Chamber of King Felipe. The earldom of Surrey had been restored to him, and as heir of a dukedom he was senior in rank.

He succeeded his grandfather in 1554. He was favored by Elizabeth I although he was jealous of the larger measure of confidence she placed in Robert Dudley, Earl of Leicester. Howard commanded the English forces that intervened in Scotland in 1559–60 and in 1568 was chief of the commission that inquired into Scottish affairs after the flight of Mary, Queen of Scots to England. A widower, he conducted secret negotiations for Mary's hand. Elizabeth heard of the project, however, and forbade it, and Norfolk was imprisoned (1569–70). On his release Howard was drawn into the plot of Ridolfi, agent of Felipe II of Spain, who was planning a Spanish invasion and the dethronement of Elizabeth. The plot was discovered, Norfolk was imprisoned (1571) in the Tower of London, tried, and beheaded.

Mary was forced to abdicate her Throne in favor of her son James VI, who later inherited the English Throne from Elizabeth I and became James I combining Scotland and England. Mary had a claim to the Throne of England through her grandmother, King Henry VIII's sister, Margaret. Elizabeth always took Mary as a serious threat, so when Mary fled Scotland for England, Elizabeth had her detained. She kept her detained for over 20 years. Finally, Elizabeth had Mary tried on charges of taking part in the plot that killed Henry, Lord Darnley, father of James VI, and with plotting the assasination of Elizabeth herself. She was executed. Attaching one's wagon to that star was foolish, to say the least.

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