Thomas was the eldest son of Thomas Courtenay, 4th Earl of Devon, and his wife, Anne, daughter of Richard, Lord Talbot, and sister of the 1st Earl of Shrewsbury. He succeeded his father as the premier nobleman of the West Country at the age of only eight. Four years later, he was knighted by King Henry VI and he served him faithfully for some years during the French Wars.

In 1441, the lucrative stewardship of the Duchy of Cornwall was given to the Earl, despite the office already having been conferred on the West Country gentleman, Sir William Bonville, four years earlier. Bonville’s growing influence at Court had been threatening Courtenay’s dominant position in Devon & Cornwall; and now violent clashes began to erupt between the two factions. The Royal Council was forced to intervene. Neither man was to be steward and both were put under large bonds to ensure good behaviour.

Between 1443 & 1447, Bonville was out of the country, serving the King in France. The Earl of Devon was restored to the Cornish stewardship in 1444 and the feud lapsed for six years. By 1450, the newly created Lord Bonville had strengthened his position at Court by aligning himself with the Royal favourite, James Butler, the Earl of Wiltshire, who was also looking to acquire further influence in Western England. Courtenay counteracted this move by allying himself to Richard, Duke of York, the rival for Henry VI’s Crown. In 1452, he was even organising pro-Yorkist riots across the West Country. He was also one of the few nobles to side with York at the confrontation at Dartford, where the Duke and his allies were forced to submit to the will of the King.

The Earl was thus imprisoned and stripped of his offices, but, in late 1453, the Duke of York was in a position to release him during one of King Henry's bouts of madness. The next year, the country was placed under York's protectorship and Courtenay felt able to resume his attacks on Bonville until the Council intervened again. During 1455, however, his alliance with York disintegrated and he became a firm Royalist on more. With the outbreak of the War of the Roses, the Earl was with the King’s army at the 1st Battle of St. Albans, at which the Duke of York destroyed his enemies and took the King into custody. The Earl of Devon, seemly impressed by the success of York’s direct action, threw the West Country into turmoil in the October by leading a several thousand strong force in attacks on Bonville's property and his servants. He even instigated the murder of Nicholas Radford. On 1st November, the Earl seized Exeter and held the city for six weeks before being compelled to surrender to York. He was imprisoned in the Tower, but was released the following year and pardoned by Queen Margaret who had re-established Royal control of the Government. Courtenay became the Queen’s great ally, though, having been a member of both factions, he felt he was in an ideal position to broker a lasting peace. In early 1458, he travelled with Queen Margaret’s entourage to the great Abbey at Abingdon where he hoped to mediate between the two sides. However, the monastery was home to a number of Yorkist sympathisers, including the Abbot, and before negotiations could begin the Earl died, it was rumoured, from poisoning.