Mostafa Ahmadi-Roshan died after an unidentified motorcyclist stuck a magnetic bomb to his vehicle, according to the Iranian media.
The 32-year-old academic had been working at the Natanz uranium enrichment facility.
Iranian officials blamed the bombing on Israel, which they claim is trying to derail the country’s nuclear programme.
Israel has denied the charge, and along with the US, claims that Iran is attempting to build a nuclear weapon.
Tehran says that the enrichment programme is for peaceful purposes.
Safarali Baratloo, deputy Tehran governor, is quoted on BBC online saying: “The bomb was a magnetic one and the same as the ones previously used for the assassination of the scientists, and the work of the Zionists [Israelis].”
The blast, the latest in a series of attacks on nuclear scientists in Iran, reportedly took place near Tehran’s Allameh Tabatai university.
Mr Ahmadi-Roshan supervised a department at Natanz uranium enrichment facility in Isfahan province, the semi-official Fars new agency reported.