Banaie is not believed to have a new role to go to although is expected to stay in advertising.
He has played a key role in establishing the Isobar network following the decision to rebrand more than 60 agencies in May 2010.
The strategic leader who turned 37 earlier this month is the latest departure from global chief executive Mark Cranmer’s Isobar team.
Glue’s founder, Mark Cridge, left his role as the global managing director in June after a six-month sabbatical, and Seb Royce, the executive creative director of Glue Isobar, exited in July.
Together they have been responsible for some of the most awarded digital campaigns in recent times, including the Nokia sign post campaign that scooped a Campaign BIG award and seven Cannes Lions in 2010.
Confirming the departure, Cranmer said: "Niku's a good guy and a great talent and I wish him all the best. He will be leaving us at the end of the month. I'm hoping he'll go on to do something really entrepreneurial."
Banaie first joined Aegis Media 11 years ago as Carat’s first head of innovation before becoming the UK’s youngest managing partner at Naked in 2003.
He rejoined Aegis at the end of 2008 with a remit to establish Sweden’s digital agency, Farfar, in London. The project was closed in 2009.
Acknowledging the transition Isobar is currently going through, Cranmer was keen to stress the arrival of Penny Herriman as chief executive at the end of last year.
A raft of other new Isobar hires includes Marc Huijbreghts as global client director, Patricia MacDonald as exec planning director, Mike Mulligan as COO and operations director, Rick Williams as CTO and Carrie Arnold as head of project management.
Cranmer said: "We are going through an exciting year as we broaden the horizons and skill base of the Uk business to meet the wider business demands of clients and our group, both locally and globally."