Abu Muhammad al-Masri was killed by two Israeli operatives on 7 August in Tehran who were acting at the behest of United States, New York Times reported.
The killing of Masri was kept secret until now.
A senior Afghan security official told Reuters that Masri was killed in the Pasdaran area of Tehran.
US authorities had been tracking him down in Iran for years, said the Times.
Al Qaeda has not announced his death yet. Moreover Iranian officials have tried to cover the matter .
Iran on Saturday denied the report and said that there were no terrorists on its soil.
US and Israeli officials have not commented on the news yet.
The Times also reported that the daughter of Masri was also killed along with him.
Masri had been living in Tehran since 2015.
Iranian media reported on August 7th that an unusual killing took place in Tehran. It said that a Lebanese man along with her daughter were killed in Tehran by unknown people.
A few weeks ago, two other senior Al Qaeda leaders were killed in Afghanistan.