The 30-year-old midfielder, who is the only surviving member of Sydney FC's inaugural squad in 2005/06, will Captain the club for the second straight season, following support from Coach Vitezslav Lavicka, the Sydney FC players and CEO Dirk Melton.
McFlynn will be joined in a leadership group by Marquee signing Brett Emerton and 2009/10 Premiership Player Karol Kisel.
"Terry was the Captain last year and did a good job so he will be the Captain again for the 2011/12 season," Lavicka said. "He has the full respect of the team and the staff and will continue in that position. Brett Emerton and Karol Kisel will be Terry's Vice Captains.
"This season we have some experienced players, from the new players and from players still with us from last season and many could be the Captain but I am very happy with Terry."
McFlynn acknowledged the confirmation that the he will wear the Captains Armband with a sense of pride and responsibility as the two-time Hyundai A-League Champions look to rebound from the 2010/11 season.
"I have always said that it is an honour and a privilege to be Captain of Sydney FC and that's certainly the case now," McFlynn said. "I am proud to say that I am the Captain of this club and I am determined to do what I can to help us get back to the top - where this club belongs.
"I'm happy to have two such experienced professionals as Brett and Karol as vice captains. They are both incredibly experienced players having played in Europe and we will all work towards setting a culture that can help us all improve, on and off the pitch.
"We're lucky that we have so many leaders in the dressing room this season and we all have the same goals."