Thomas Lee (c. 1551 – 14 February 1601) was an English army captain, who served under Queen Elizabeth I and spent most of his career in Ireland during the Tudor conquest of that country. Although of middle rank, he played a turbulent role in the factional politics of the time and was highly active during the Nine Years' War (1595–1603). He was put to death at Tyburn for his involvement in the treason of the 2nd Earl of Essex.