Majid Jamali Fashi, 24, was convicted of killing Professor Massoud Ali Mohammadi by detonating a bomb outside his home in January 2010.
Fashi was also accused of being a spy for the Israeli intelligence agency Mossad and receiving $120,000 (£72,000) for the killing.
Israel does not comment on such claims.
"Majid Jamali Fashi, the Mossad spy and the person who assassinated Masoud Ali Mohammadi, our nation's nuclear scientist was hanged on Tuesday morning," Iran's Irna news agency reported.
Professor Massoud Ali Mohammadi was a particle physics professor at Tehran University. He is one of several high-profile nuclear scientists to have been killed in Tehran in recent years.