Majid Jamali Fashi, the man accused of killing an Iranian scientist, was hanged Tuesday morning, according to Iranian State TV.
The 24-year-old was convicted of killing a Tehran University physics professor with a bomb-rigged motorcycle that exploded as he was leaving for work in January 2010.
The Iranian government also accused Fashi of being an agent of Mossad, an Israeli spy agency.
At least five Iranian nuclear scientists have been killed in recent years.
In a letter to the United Nations, Iran blamed Israel and the United States for the attempts to disrupt its nuclear program.
"There is firm evidence that certain foreign quarters are behind such assassinations," the letter said. "It is highly expected from the secretary-general of the United Nations, and president of the Security Council of the United Nations, as well as all other relevant organs and bodies, to condemn, in the strongest terms, these inhumane terrorist acts."
Secretary of State Hillary Clinton has denied such accusations.
"I want to categorically deny any United States involvement in any kind of act of violence inside Iran," she said in January.