Javid Dehghan Khalad was put to death early in the morning in the restive southeastern province of Sistan-Baluchistan, Mizan Online reported.
It comes a day after the United Nations had appealed to Iran not to go ahead with the execution of the 31-year-old.
Mizan said Dehghan was arrested in June 2015 and later convicted of being “one of the leaders” of a “terrorist” group linked to the jihadist Jaish al-Adl (Army of Justice).
Also known as Mohammad Omar, he had been found guilty of carrying out “armed action against the state”, the website said.
Dehghan was found to have been involved in the killing of two Revolutionary Guards’ members in 2015, as well as leading a raid aiming to abduct five border guards, one of whom was killed, it added.
The UN had on Friday urged Iran to halt the execution as it rebuked the Islamic republic for a spate of recent hangings, including of members of minority groups.
“We urge the authorities to halt the imminent execution of Javid Dehghan, to review his and other death penalty cases in line with human rights law,” the Geneva-based Office of the United Nations High Commissioner for Human Rights wrote on Twitter.
“We strongly condemn the series of executions — at least 28 — since mid-December, including of people from minority groups,” it added.
London-based rights group Amnesty International has alleged Dehghan’s trial was “grossly unfair” with the court relying on “torture-tainted confessions” and ignoring abuses committed during the investigation.
Jaish al-Adl has carried out several high-profile bombings and abductions in Iran in recent years.
In February 2019, 27 members of Iran’s Islamic Revolutionary Guard Corps were killed in a suicide attack claimed by the group.
Jaish al-Adl was formed in 2012 as a successor to Sunni extremist group Jundallah (Soldiers of God), which waged a deadly insurgency for a decade before it was severely weakened by the capture and execution of its leader Abdolmalek Rigi in 2010.
The Islamic republic has come under fire over a series of executions since late last year of high profile figures, including the formerly France-based dissident Ruhollah Zam on December 12 and wrestler Navid Afkari on September 12.