Shahram Amiri's flight from Qatar landed in Tehran in the early hours of Thursday morning.
The US state department has insisted he was in the US of his own free will.
In June, Mr Amiri appeared in three videos giving conflicting stories about how he had arrived in the US.
He said in the first that he had been kidnapped by CIA and Saudi agents while on a pilgrimage.
In the second message he said he had gone to the US to improve his education and was living freely in Arizona.
In the third, he claimed to have escaped from US custody.
On Monday evening Mr Amiri arrived at the Iranian Interests Section of the Pakistani embassy in Washington, which handles Iranian affairs in the US capital, and asked to be repatriated.
Since then, he has renewed his allegations that he was kidnapped, giving more details in an interview from the Iranian diplomatic mission with a Danish TV company.
He said he was abducted while on a pilgrimage to Saudi Arabia.
"A white van stopped in front of me... They told me in Farsi that they were part of another group of pilgrims and said 'We are going towards a mosque and we will be happy to take you as well'," he told Atlantic TV.
"When I opened the door to get in and sit down, the person at the back put a gun to my side and said 'Please be quiet, don't make any noise'."
He said he was drugged and woke up in a military plane which took him to "American territory".