The first Duke of Estonia ( ) was appointed in 1220 by Valdemar II after Danish conquest of Estonia during Livonian crusade. The title was resumed by the kings of Denmark since 1269. For the period of 1266-82 during the reign of Queen Dowager Margaret Sambiria the title Lady of Estonia () was used.
In 1332 after Christopher II died his elder son Otto inherited the title of the Duke of Estonia. Valdemar III assumed the title in 1338.

The Duke of Estonia rarely resided in Estonia. To govern the Duchy of Estonia the king of Denmark appointed together with royal counsellors the Lieutenant () who resided in Reval.

The king of Denmark sold the Duchy to Teutonic Order in 1346 but Christian I reassumed the title of duke of Estonia in 1456.

After the Livonian War Estonia became part of Swedish Empire and the title was gained by kings of Sweden.

The title was resumed by the Russian tsars after the Great Northern War and Treaty of Nystad when Estonia became part of Russian Empire. The last Duke of Estonia () was Nicholas II of Russia.