The 33-year-old's impact on the field in 2013-14 has been curtailed by injury, but there is no denying the former captain's influence off the field at a club where stability has been at a premium in recent years.
With marquee skipper Alessandro Del Piero also due to call it quits, the club have a leadership vacuum to fill. Centre-back Sasa Ognenovski, who joined in January and has already agreed a deal to stay on in 2014-15, looms as a candidate to inherit the armband.
However, with the future of coach Frank Farina uncertain and the club's supporters and hierarchy casting envious glances at the unity and identity established so quickly at cross-city rivals Western Sydney, there can be no room for error in the transfer market or the boardroom if the Sky Blues are re-establish themselves as one of the competition's genuine powerhouses.
McFlynn meanwhile, who has not played since injuring himself in Sydney's 5-0 Australia Day win at Melbourne Victory, bows out as a fan favourite and club stalwart, with the grudging respect of rival clubs' supporters after winning championships in 2006 and 2010.
"It has been a privilege and an honour to represent Sydney FC for nine seasons and I have felt immense pride every time I have pulled on the sky blue shirt," he said in a statement.
"I have had some fantastic times and been part of some incredible moments in Sydney FC's history which I will never forget, and I would like to thank everyone at the club for giving me the opportunity to experience them.
"Sydney FC will always have a special place in my heart and I've made lots of lifelong friends both on and off the field through this great club. I'll always be thankful to the club for that opportunity."
Sydney defeated Wellington 4-1 at home on Sunday to close in on a top-six berth.
They will need to impress in the finals to avoid the season being remembered for dressing room unrest involving Matt Thompson and Nick Carle, as well as virulent fan discontent being directed at Farina and chairman Scott Barlow.
