A T67 "Firefly aircraft crashed this morning, killing a Jordanian lieutenant colonel and his Iraqi trainee, during a routine training excercise" said Colonel Mamdouh al-Amiri, spokesman for the Jordanian military.
He said the crash occurred over Jordanian soil but did not elaborate on the cause of the accident or its location.
The Jordanian military regularly trains Iraqi pilots as part of defence agreements between the two countries, Amiri said.
Local media reported that the crash took place some 70 to 90 kilometres north of the capital Amman.
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In February, it extended air strikes against IS to Iraq after the group released a video of downed F-16 pilot Maaz al-Kassasbeh being burned alive.
Last year a Jordanian air force pilot was killed when his F5 aircraft crashed in eastern Jordan during a training mission.
In 2013 a T67 Firefly crashed in the north of the kingdom because ot technical problems, killing the pilot and a trainee.