The visit comes as tensions are running high with neighbouring Russia over its role in the conflict in Ukraine.
The jets landed at noon at the Amari airbase, which currently also hosts German fighters belonging to NATO's Baltic Air Policing mission, created to help small Baltic members protect their borders with Russia.
Estonian Air Force public affairs officer Alar Laats told AFP the visit would last only a matter of hours and was for training purposes.
The move is likely to be viewed as provocative by Russia which regularly sends its own fighter aircraft close to the borders of the three Baltic states of Estonia, Latvia and Lithuania, sometimes even encroaching onto Estonian airspace.
The US confirmed on Tuesday that for two weeks it would be operating a pair of stealth drones from the Lielvarde airbase in Latvia, while neighbouring Lithuania is currently hosting Hungarian aircraft at the Siauliai airbase as another component of the NATO Baltic Air Policing mission.
Kiev government troops have been fighting pro-Russian separatists since April last year sparking the highest East-West tensions since the Cold War ended more than two decades ago.
The West has accused Russia of not only arming the rebels but sending in troops to support them. Moscow denies the charges.
The F-22 is virtually undetectable by radar. It became operational in 2005 and was used in combat for the first time in September last year in strikes against Islamic State jihadists in Iraq and Syria.
The US Air Force has a fleet of about 180 F-22s.
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