Materials science professor Sirous Asgari, 59, was indicted by US federal prosecutors in April 2016. A federal judge in Ohio acquitted Asgari in November 2019.
Tehran and Washington have denied reports that his release was part of a prisoner swap.
US authorities said in May that Asgari, who tested positive for the novel coronavirus in April, would be deported once he received medical clearance.
Photos published by Iranian state media showed Asgari being reunited with his family in Tehran on Wednesday.
Last year, Iran freed US citizen Xiyue Wang, who had been held for three years on spying charges, and the United States released Iranian Massoud Soleimani, who faced charges of violating US sanctions on Iran.
The outbreak of the novel coronavirus has led Iran, one of the worst-hit countries in the Middle East, to temporarily release some prisoners in a bid to curb the spread of infections.
In mid-March, US Secretary of State Mike Pompeo said Tehran was considering freeing some US citizens as Michael White, a US navy veteran who has been detained in Iran since 2018, was released from prison on medical furlough. He remains in Iran.
It is not clear exactly how many Americans-Iranians are being held in Iran, but they include father and son Baquer and Siamak Namazi.
Michael White, a US navy veteran who was detained in Iran in 2018, have been released from prison since mid-March on furlough but remains in Iran.
Several dozen Iranians are being held in US prisons, many of them for breaking sanctions.Iran’s Foreign Minister Mohammad Javad Zarif said in December that Tehran was ready for a full prisoner exchange with the United States, tweeting: "The ball is in the US'