The unnamed men were accused of involvement in deadly bombings in oil-rich Khuzestan Province more than a year ago. The province, which borders Iraq, has a large Arab population.
The EU called on Tehran earlier this month to refrain from executing the three men.
In January, authorities in Ahwaz hanged four men facing similar charges. Three other Arab men were salso executed in December for alleged involvement in the attacks.
Dissident Arab activists in Khuzestan have accused the government of setting up trump charges against Arab activists fighting against Tehrans repressive policies.
A string of top Iranian officials, including hard-line President Ahmadinejad, have accused Britain of being behind the bombings in Ahwaz. Tehran has repeatedly accused the British secret services of training ethnic Iranian Arabs in southern Iraq and sending them to Iran to carry out sabotage operations.
London has repeatedly denied any involvement in the events in the region.
