McFlynn began his footballing career in England as an apprentice at
Queens Park Rangers in 1996. McFlynn made only two first-team appearances in his five-year stay at the club – his first-team debut was made on 28 April 2001. He was released in 2001 and signed for
Woking. McFlynn made 10 appearances for the West Surrey club scoring only once, in a short half-year deal. McFlynn moved to
Margate, initially on a one-month loan deal, but ended up being a useful three-year career, in November 2001. McFlynn quickly became a huge favourite with the Margate fans, helped by a stunning debut goal against
Boston United. He made 63 appearances for the club and scoring a total of 11 goals. A hamstring injury late in 2002 saw McFlynn miss several key games and as a result was sold to
Morecambe. In 2003, McFlynn moved to Conference rivals
Morecambe for £14,000 and, despite scoring on debut, he was unable to cement a spot in the team and was released in 2005, but made 35 appearances and scoring five goals in just 17 games.
Sydney FC Following the advice of former teammate and one-time
New Zealand captain
Chris Zoricich, McFlynn moved to Australia to play in the newly formed
A-League and was signed by
Sydney FC manager
Pierre Littbarski after a successful trial in February 2005. In his first season with Sydney FC, McFlynn made 21 appearances and proved to be a strong and determined player. He scored a memorable first goal for the club in round five of the
2005–06 season against the
Queensland Roar in which he lobbed their goalkeeper,
Tom Willis, from 30 meters out to round off a 3–1 victory to Sydney FC. Sydney FC progressed to the
inaugural A-League Grand Final, which was played at the
Sydney Football Stadium on 5 March 2006. McFlynn played the full 90 minutes as Sydney FC defeated the
Central Coast Mariners 1–0 in front of 41,689 spectators to become the inaugural A-League champions. He failed to make an impact on the 2006–07 A-League season when he picked up a hamstring injury and as a result, only making 13 appearances, without scoring. In the
2007–08 season he scored two more goals. One against Central Coast Mariners, in Sydney's 5–4 win and against
Wellington Phoenix which Sydney won 2–0. Both of these goals were in the latter half of the season. In February 2008 McFlynn signed a new contract with Sydney for a further two years. He scored his fourth goal in Sydney's fifth match in the
A-League 2008-09, against
Adelaide United in Sydney's 3–0 victory, with a volley from outside the box. Another goal for Sydney against F3 Freeway rivals Central Coast Mariners took his tally to five. In a match against
Adelaide United at
Hindmarsh Stadium in which he was given a straight
red card he sustained five-week knee injury. However, he returned to the bench in the third game of the season against
Adelaide United in their 2–0 loss at the
Adelaide Oval. His sixth goal for the club came against rivals Central Coast Mariners, scoring the only goal in their 1–0 victory. Speaking after the game McFlynn said it was his most memorable, as his first child had been born the week before, not to mention it was his first game after returning from a thigh injury. In November 2009, Sydney FC held a press conference to inform the public that they had re-signed McFlynn on a further three-year contract, up until 2013. This will mean by the end of this contract, McFlynn will have been with the club for eight years. McFlynn further commented saying I don't want to play football for any other clubs, either in Australia or anywhere else," he said "I've been at Sydney FC for five years and I couldn't be happier to be signing on for another three years. "I have grown to love the club, my family is here and I see Sydney as my home." On 26 February 2010 it was announced that he had received permanent Australian residency. McFlynn eventually gained
Australian citizenship. One of his greatest honours was standing in as captain for the
Grand final as
Steve Corica and
John Aloisi were injured. He was officially awarded the captaincy for the 2010–11 season on 22 July. His 100th A-League game for Sydney FC came in Round 3 of the
A-League 2010-11 season, with Sydney losing 1–0 to
Brisbane Roar at
Suncorp Stadium. McFlynn led Sydney FC into their first game of the
AFC Champions League against
K-League club
Suwon Samsung Bluewings FC. However his role would end after just 32 minutes when he was
sent off for
stomping on Korean player
Lee Sang-ho. After a two-match suspension, he returned to the senior team to help lead Sydney FC to a 3–2 victory over
Shanghai Shenhua in
Shanghai. After captaining Sydney to the
2011–12 A-League finals, McFlynn made his 150th appearance in the semi-final against
Wellington Phoenix at
Westpac Stadium, although Wellington defeated Sydney 3–2 and knocked them out of the finals in the process. On 6 April 2014, McFlynn announced he would leave Sydney FC and retire from A-League football.
Bonnyrigg White Eagles McFlynn joined reigning
NSW Premier League Champions
Bonnyrigg White Eagles making his debut on 11 May 2014 in a round nine clash against
Blacktown City Demons. ==Post playing career==