Thomas Lee (1551/1552 - 1601) is an English army captain, who serves under Queen Elizabeth I and spends most of his career in Ireland during the Tudor conquest of that country.

Although of middle rank, he plays a turbulent role in the factional politics of the time and is highly active during the Nine Years war (1595-1603).

He is put to death at Tyburn for his involvement in the treason of the 2nd Earl of Essex.