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.
'New provocation' The US, Israel and many Western nations have opposed Iran's atomic programme, fearing it may be a front to creating a nuclear bomb.
Iran insists its nuclear programme is for purely peaceful purposes.
This week, Iran said it was installing newer and faster centrifuges at its nuclear plants, with the goal of speeding up its uranium enrichment process.
Enriched uranium can be used for civilian nuclear purposes, but also to build atomic bombs.
The French government condemned the move as a "new provocation".