The eldest son and heir of the UK's head of state, King Charles III, will meet members of the Mercian Regiment at the Tapa base to "learn about how they are bolstering NATO's eastern flank", the palace said in a statement.
William, 42, will also meet Estonian soldiers.
There are approximately 900 British military personnel in Estonia, the country's largest permanent deployment abroad.
The visit comes as several European countries, including the UK, have expressed a need to strengthen the continent's defence as the United States shifts resources and focus to other parts of the world.
The prince's visit to Estonia -- his first to the EU and NATO member country -- will begin with a meeting with President Alar Karis.
He will also visit a school for Ukrainian children who fled their country after it was invaded by Russia.
William, whose Earthshot Prize initiative champions measures to combat climate change, will also attend a workshop with a series of startups specialising in renewable energy.
The Baltic states of Lithuania, Latvia, and Estonia completed their integration into the main European electricity grid in February, after disconnecting from the Russian-controlled grid over fears it opened them to blackmail from Moscow.
The move gives them the opportunity to integrate more renewables into their energy mix, the palace said.
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