The 57-year-old most recently worked as assistant head coach at Fulham last season under Rene Meulensteen.
Wilkins will take charge of the team after their friendlies against Uzbekistan on Thursday and China five days later.
His first match in charge will be against Malaysia in Kuala Lumpur on October 11.
The former England midfielder will lead the team lead the team at the 2015 AFC Asian Cup in Australia where Jordan are in the same group as Japan, Iraq and Palestine.
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