The 35-year old will end his tenure with the Townsville club at the end of the season and will return home to Scotland citing family reasons for his decision.
McLaren joined fellow Scot Ian Ferguson at the Fury from QSL side Brisbane Strikers (where he was head coach) in May 2010 and remained in his role when Czech tactician Franz Straka joined the club.
McLaren will finish up after this weekend's clash with the Wellington Phoenix and is confident he leaves the struggling club in a strong position.
"It's with great sadness that I will be leaving the club and the region after our match against Wellington Phoenix," he said.
"I've thoroughly enjoyed the opportunity to work for the Fury even through the eventful season we've had.
"I want to make it clear that this has been a difficult decision to make and has nothing to do with the club's current plight, but as all husbands and fathers know, family must be the priority.
"I hope to continue to contribute to the club whilst based overseas and if circumstances allow, return to Townsville and Fury in the coming years.
"I'd like to wish Fury much success and I'm 100% confident this club will have a long and bright future."