"We have referred the file of the five accused, who are Arab nationals, to the state security court to try them in the case of the terrorist bombings of Rukban," Judge Ziad al-Edwan said.
He said the trial would open "within days".
IS claimed the suicide bombing last June 21 that killed seven soldiers at a military post in Rukban, near a no man's land area where thousands of Syrian refugees are now stranded and where the frontiers of Iraq, Syria and Jordan meet.
Amman had not previously announced any arrests in connection with the attack.
"It seems they belong to the Daesh terrorist gang and are linked to the bombings through planning with the suicide attacker who carried it out," the judge said, using an Arabic acronym for IS.
Edwan said the five accused had monitored the border, chosen the time of the attack and the route to be taken by the explosives-rigged car, as well as having filmed the attack.
Soon after the attack, the army declared Jordan's desert regions that stretch northeast to Syria and east to Iraq "closed military zones", stranding refugees in no man's land.
The June bombing came two weeks after a gunman killed five Jordanian intelligence officers in a Palestinian refugee camp north of the capital.
The UN refugee agency says it has registered more than 650,000 Syrian refugees in Jordan since Syria's war broke out in 2011. Amman says it hosts 1.3 million Syrian refugees.
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