Aitken has left the club to team up with David O'Leary, with whom he worked with during their days together at local rivals Aston Villa, at United Arab Emirates outfit Al Ahli.
He had assisted manager Blues Alex McLeish during his time as the manager of the Scottish national side and joined him at St Andrews in November 2007.
"Naturally I am very disappointed to lose an extremely valued member of Birmingham City Football Club," McLeish told the club's official website.
"He is respected by everyone at the club. "I have got a great relationship with Roy and he is well liked and respected by the players.
"But he has received an offer that he couldn't refuse and I totally understand the decision he has made for himself and his family.
"Roy goes with my thanks and blessings. He is not just someone I've worked with for some time now but also an extremely good friend and I wish him all the best in his new challenge."