Shahram Amiri was hanged after allegedly giving America information about the Islamic republic’s nuclear programme.
He revealed to “the enemy”, according to a judicial spokesman, who claimed Tehran had “outsmarted” America.
News of his reported death comes a year after his country agreed a landmark agreement with the West to limit uranium enrichment in exchange for lifting economic sanctions.
Mr Amiri, who had worked for a university affiliated to Iran’s , vanished in June 2009 while on a pilgrimage to holy sites in Saudi Arabia.
He resurfaced a year later in the US when he appeared in a set of online videos.
Mr Amiri then walked into the Iranian interests section at the Pakistani Embassy in Washington and demanded to be sent home, returning to a hero’s welcome in Tehran.
Back in the Islamic republic, he said he had been held in the US for more than a year after being “kidnapped” at gunpoint by two Farsi-speaking agents in Medina.
Mr Amiri was detained in Iran in 2010 and judicial spokesman Gholamhossein Mohseni Ejeie said he was tried in accordance with the law and had access to a lawyer.
He denied having any information, saying: “I’m not involved in any confidential jobs. I am a simple researcher who was working in the university.”
But Mr Amiri, aged in his late 30s, was convicted of handing over “confidential and vital” information to the US.
“He appealed his death sentence based on judicial process. The Supreme Court… confirmed it after meticulous reviews,” Mr Ejeie added.
US officials said in 2010 Mr Amiri was paid $5m (£3.8m) to offer the information about Iran’s nuclear programme, though he left the country without the money.
They said Amiri, who ran a radiation detection programme in Iran, stayed in the US for months under his own free will.
Some analysts suggested Iranian authorities may have threatened Amiri’s family back in Iran, forcing him to return.
It is not known what prompted Iranian authorities to execute him, years after his first disappearance.
However, since the nuclear deal, hardliners in Iran’s government have increasingly targeted dual nationals for arrest and cracked down on journalists, artists, human rights activists and others.