Isna news agency named him as Daryoush Rezaei, 35, adding that his wife was wounded and rushed to hospital.
In 2010, nuclear scientist Massoud Ali Mohammadi was killed by a remote-controlled bomb in Tehran.
Iran blamed that attack on Israeli secret service Mossad. Israel has long warned about Iran's nuclear programme.
Some reports said the latest attack involved assailants on a motorcycle, who shot him in the neck in front of his house.
Mr Rezaei was said to be a physicist at a Tehran university, where media reports described him variously as a teacher, researcher and student.
Several have linked him to the country's nuclear programme.
Isna said that Mr Rezaei was an expert with links to the Atomic Energy Organisation of Iran.
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