Shahram Amiri arrived at Tehran's Imam Khomeini Airport and was greeted by Deputy Foreign Minister Hassan Qashqavi, according to the Islamic Republic News Agency.
Upon arrival, Amiri, who is a researcher from Tehran's Malek Ashtar University, repeated his claim that he was kidnapped by U.S. intelligence agents while on a religious pilgrimage to Saudi Arabia in June 2009.
"I was abducted in Medina ... Then I was transferred to an unknown location in Saudi Arabia," Amiri told Press TV. "They injected anesthetic drugs into me. They took me to the United States on a military plane.
"During my stay in the first two months, I was subjected to heavy psychological and mental tortures by CIA interrogators," he said. "Other kinds of pressure too. They told me if I don't cooperate with them, they will hand me over to Israel and there are hidden prisons in Israel and there will be no trace of you any more."
On Monday, Amiri went to Iran's Interest Section at the Pakistani Embassy in Washington and asked to be sent home.
The Iranian government has accused the United States of involvement in Amiri's disappearance, saying the researcher was taken to force him to give up data about Tehran's nuclear program.
A top Iranian lawmaker recently claimed that newly found documents back up Tehran's claims that the CIA is responsible for Amiri's disappearance, Iranian media reported Sunday.
Javad Jahangirzadeh, a member of Iranian parliament's National Security and Foreign Policy Commission, said Iranian officials had turned over the documents to the Swiss ambassador in Tehran.
The U.S. State Department has denied that charge.
A U.S. official, who is not authorized to talk to the media about such issues, told CNN last month that it would be "ludicrous, absurd and even preposterous" to claim an individual was kidnapped by the United States and held against his will.
Last month, two videos surfaced on the Internet of a man claiming to be Amiri, in which he said he had escaped from U.S. agents and was hiding in Virginia.
That was the third time that videos allegedly showing Amiri had been circulated on the Internet.
CNN could not independently verify the authenticity of the videos, nor the identity of the man in them.
"If he is who people think he is, the U.S. would be in contact with the person," a CIA official said last month. And if he were being held against his will, "how would he have been able to produce any of the videos?" the official said.
Tehran blamed Washington for Amiri's disappearance shortly after revelations surfaced that Iran has been building a second uranium enrichment facility near the city of Qom. After that, tensions over Iran's nuclear program mounted.
Iran claims its nuclear energy is solely for civilian purposes. But the United States has pushed the United Nations to punish Tehran for its nuclear ambitions. The Security Council recently slapped a fourth round of tough sanctions on the Islamic republic.
It is unclear how much information Amiri was privy to in Iran.