Southampton Flahavan began his career at
Southampton. He was named as an unused substitute several times in the
Premier League, but did not make a first team appearance, being behind
Paul Jones,
Dave Beasant and
Maik Taylor in the pecking order. He left Saints on a free transfer in 1998, and went on to make his name with
Conference side
Woking.
Southend United He was signed by Southend in October 2000. Flahavan played for Southend during two spells and in total made 356 appearances for the club helping them from League Two into the Championship in back-to-back seasons. Flahavan was seen as one of the main reasons behind the club's rise through the divisions. Flahavan put in a man of the match display against
Manchester United in the
League Cup on 7 November 2006, making a string of saves from
Cristiano Ronaldo and
Wayne Rooney. Southend won the game 1–0 with a
Freddy Eastwood free kick. Southend were eventually knocked out the competition in the quarter-finals to Tottenham Hotspur at White Hart Lane 1–0 where again Flahavan produced another man of the match display.
Crystal Palace Flahavan signed for
Championship side
Crystal Palace in early July 2008 on a
Bosman ruling free transfer, signing a three-year contract to compete for the first team shirt with
Julián Speroni. He rejected Southend's offer of a one-year deal. Flahavan made his debut in Palace's 2–1
League Cup win over
Hereford United in August 2008. Flahavan also played in the next round against
Leeds United, but Palace lost the game 4–0. Flahavan's only league appearance of that season came against
Cardiff City and despite saving a penalty, Palace lost the game 2–1. The following season saw Flahavan remain at the club despite speculation linking him with a move away, and he made a first home league appearance for the Eagles in the 0–2 home defeat to
Newcastle United, with Speroni ruled out through injury. This proved to be his last appearance for the Eagles.
Loan to Leeds United On 26 March 2009, he joined
Leeds United on loan until the end of the 2008–09 season, although due to an early injury he did not feature for Leeds United, who also had goalkeepers
Casper Ankergren,
David Lucas and
Alan Martin already at the club.
Loan to Oldham Athletic Oldham Athletic signed Flahavan on a month emergency loan in November 2009. Flahavan made his Oldham debut in the FA Cup loss against his former club Leeds United. His loan was later extended until the end of the season, he picked up the Latics' player of the month in April 2010 and went on to play 20 games for the club.
Portsmouth On 8 August 2010, Flahavan started training with
Portsmouth ahead of a possible move to the club his older brother
Aaron played for. On 27 August, Portsmouth signed Flahavan on a one-month deal. He was given the number 37 jersey. Flahavan signed a new one-month deal at
Fratton Park on 23 September and then did so again on 26 October. He later extended his contract until the end of the season. Flahavan did not play a single match in the 2010–11 season, as
Jamie Ashdown played the full 90 minutes in all 50 of Portsmouth's matches. He left upon the expiration of his contract in June.
AFC Bournemouth in 2013. On 28 June 2011, Flahavan signed a one-year deal with
AFC Bournemouth with a further one-year extension in the club's favour. Flahavan looked forward to working with
Lee Bradbury and goalkeeping coach
Neil Moss, and was expected to provide competition for
Shwan Jalal. He signed a new one-year contract in January 2012. Flahavan played in all but two of Bournemouth's 46 league games in the 2011–12 season. The following season Flahavan picked up a shoulder injury in pre-season which ruled him out of the 2012–13 season. In May 2013, Flahavan signed a new one-year deal under manager Eddie Howe. In May 2015, Flahavan left Bournemouth in order to pursue regular first-team football.
Crawley Town After his release, Flahavan signed for
Crawley Town on a short-term deal. He kept a clean sheet in a 1–0 victory over
York City on
Halloween. He left Crawley in January 2016. ==Coaching career==