Wilkins will take over the running of the team next week when they return home after playing friendlies in Uzbekistan and China.
The JFA also announced that former Irish international Frank Stapleton had been appointed as his assistant.
"The decision was taken under the guidance of JFA President HRH Prince Ali Bin Al-Hussein, who was trusted by the JFA Executive Board to choose the suitable candidate for the Jordan National Team’s coaching post due to his great vision in leading Jordanian Football towards success..." the JFA announced.
Jordan's current coaching staff, consisting of Ahmad Abdul Qader, Anzor Hina, Waleed Michael and Manuel Barriounuevo, would all be retained although their exact roles were not revealed.
Wilkins, 57, emerged as the frontrunner for the role after attending a team training session last week with Prince Ali, the son of Jordan's late King Hussein and Queen Alia.
His appointment comes less than five months before the AFC Asian Cup in Australia, which Jordan has qualified for, in the same group as South Korea, United Arab Emirates and Saudi Arabia.
Wilkins won 84 caps for England during his playing days, which spanned more than two decades. He played as a midfielder for a handful of different teams, including Manchester United, Chelsea and Queens Park Rangers.
He began coaching in 1994 and worked as an assistant with several teams, including Fulham, Chelsea, Watford and Millwall.
He returned to Fulham as an assistant coach in 2013 before leaving the post earlier this year.
Stapleton spent most of his playing career at Arsenal and Manchester United, winning FA Cups for both clubs, and earning 71 caps for Ireland.
He switched to coaching in 1991, spending four seasons in charge of Bradford City and one in American Major League Soccer.
(Reporting by Julian Linden in Singapore; editing by Amlan Chakraborty)
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