Shahram Amiri had been in custody in Iran since 2010.
"Shahram Amiri had access to the system's top secrets and had gotten connected with our number one enemy the Great Satan," Iranian judicial spokesman Hojjat al-Eslam Mehdi Mohseni-Ejehei told reporters Sunday, according to state news agency IRNA.
Amiri's case had been reviewed by the Iranian high court, which upheld the conviction, according to Mohseni-Ejehei. "The Iranian High Court reviewed this decision with extreme care given the allegations of espionage," he said.
The charge of treason in Iran could result in anything between 10 years in prison and the death penalty, Mohseni-Ejehei explained. But since the beginning of Amiri's case, all lower courts have ruled to execute, he added, according to IRNA.
Amiri vanished in 2009 during a religious pilgrimage to Saudi Arabia. Tehran accused Washington of abducting him -- an accusation the U.S. denied.
A year later, videos surfaced online showing a man claiming to be the scientist. In them he denied being a defector and claimed to have been hiding out from CIA operatives in the U.S. state of Virginia.
In a subsequent video, however, he said he was living freely in Arizona.
Two weeks later, on July 14, 2010, CNN reported that Amiri had returned to Tehran after going to Iran's interest section at the embassy of Pakistan in Washington. He repeated his claim that he was kidnapped by American intelligence operatives.
In an interview with Iranian state-run Press TV, Amiri said he faced "psychological warfare and pressure that are much worse than being in prison."
But U.S. officials at the time said Amiri had defected voluntarily and provided "useful information to the United States," a claim supported by emails sent to Hilary Clinton -- then Secretary of State -- and released by the U.S. State Department last year.
In July last year, Iran agreed to rein in its nuclear program following a landmark agreement -- called the Joint Comprehensive Plan of Action -- with the P5+1 group of world powers, including the United States, UK, France, China and Russia plus Germany.
Under the terms of the deal, Iran would reduce its uranium stockpile by roughly 98%, phase out its centrifuges over the next 15 years, limit research activities, allow heightened inspections and ship spent fuel outside of the country.
And in return, many of the crippling international sanction against the country would be lifted.
Critics warned the terms of the agreement negotiated with Iran -- essentially designed to thwart the development of nuclear weapons -- are time-restricted, meaning the international community, to a certain extent, is kicking the can down the road, hoping that Iran will not want to risk being frozen out economically once again.