Milligan, one of the mainstays in the line-up of Socceroos coach Ange Postecoglou, has penned a two-year, multi-million-dollar deal with the Abu Dhabi-based club which finished eighth on the ladder last season and was once home to Sydney FC’s Nicky Carle.
It's understood that Melbourne Victory, which fought hard to keep its Australian marquee, accepted a transfer fee of $1 million – the figure which triggered a mandatory transfer clause in Milligan's contract.
Milligan jetted to the Middle East ahead of Australia's 2-1 FIFA World Cup win over Kyrgyzstan to meet club officials and receive a guided tour of the club's facilities, and is currently still in Melbourne awaiting final confirmation of the move.
In what has been a protracted courtship, Milligan originally turned Baniyas down in June 2013 before it came calling again in January 2014, with a transfer fee unable to be agreed.
"Mark will be joining Baniyas but there are still a few more formalities to complete yet before Mark can comment," said his agent Buddy Farah on Tuesday evening.
Milligan is expected to join his new team-mates next month in preparation for next season, and is backing himself to maintain his starting spot for the national team, despite moving to a region not regarded with the same esteem as Europe by Postecoglou.