The move was seen by Estonian defence officials as a gesture underscoring Washington's commitment to its NATO partners.
Rhetoric by US President Donald Trump, who called NATO "obsolete" shortly before he took office, deeply rattled the alliance's easternmost members bordering Russia. Trump has since reversed much of his criticism.
"Using the most modern fighter jets of the United States in Europe guarantees the sovereignty of all NATO member states," Estonian Defence Minister Margus Tsahkna said quoted by the local Baltic News Service.
"We share the same values and are ready to protect the territory of NATO member states from any kind of possible aggression," he added, speaking at Estonia's Amari air base where the jets landed.
F-35s, devised to have radar-evasive abilities, are billed as the most advanced warplanes of their kind.
The US Air Force deployed the multi-role fighters to Europe earlier this month for joint exercises NATO partners.
"I think the role of the training deployments being run by the United States Air force is to demonstrate the unique capabilities of the F-35 as they start to integrate into European operations with all the NATO and European partners," Air Marshal Stuart Evans, deputy commander of NATO’s Allied Air Command (AIRCOM), told AFP at the Amari base.
NATO is currently deploying four battalions for the first time to Poland and Baltic states Estonia, Latvia and Lithuania as tripwires against any Russian interference on its eastern flank, a region formerly under Moscow's control and spooked by its actions in Ukraine.
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