Two of the men executed were convicted of the abduction, bombing, murder of security forces and civilians, and of working with a militant group.
Iran has hanged two men for "terrorist acts" and another for murder and armed robbery.
The three were executed early on Sunday morning in the southeastern Sistan-Baluchistan province, the judiciary's official Mizan Online news agency said..
Two were named as Hassan Dehvari and Elias Qalandarzehi, arrested in April 2014 after being found with "a large amount of explosives" and weapons.
The pair were convicted of the abduction, bombing, murder of security forces and civilians, and of working with the militant Jaish al Adl ("Army of Justice") group, Mizan said.
Dehvari and Qalandarzehi were also arrested in possession of documents from Jaish al Adl on "how to make bombs" as well as "takfiri fatwas", terms used by Iran's Shia authorities to refer to decrees issued by Sunni militants.
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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 Revolutionary Guards 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 third man executed was named as Omid Mahmoudzehi. He was convicted of armed robbery and the murder of civilians, Mizan said.