Iranian Justice Minister Jamal Karimirad said that Hojat Zamani, whom he described as a terrorist, was executed two weeks ago, on 7 February.
RFE/RL's Radio Farda had reported Zamani's execution last week.
Zamani was sentenced to death for the bombing in 1998 of a Tehran court. Three people were killed in the attack.
Amnesty International had expressed concerns that Zamani may have been denied adequate legal defense and cited a Mujahedin Khalq report that Zamani had been tortured.