Flinders has played for Barnsley, Crystal Palace, Gillingham, Brighton & Hove Albion, Yeovil Town, Blackpool, Falkirk, Hartlepool United, York City and Macclesfield Town. He has also played for the England national under-20 team.
Born in Rotherham, South Yorkshire, Flinders started out at Barnsley, making his first-team debut in 2005, when he replaced the injured Ross Turnbull in the Barnsley goal. He made an instant impression, and played eleven matches in the next three months.
In the 2005–06 season, he was picked to play for a "Football League XI", in a match against their Italian counterparts. He also went back to being second choice at Barnsley, this time to Nick Colgan and was an unused substitute in Barnsley's play-off final win against Swansea City. Because of this, he only made a few more league and cup appearances in which he again impressed, leading to trials at Chelsea and Wigan Athletic. Flinders moved to Crystal Palace as part of a deal that took Sam Togwell to Barnsley in the summer of 2006.
Flinders' transfer fee from Barnsley to Palace was believed to be for £250,000 but with a potential to rise to £1 million depending on appearances.
Flinders made his competitive debut for Palace in a League Cup tie with Notts County, playing the full match as Palace were beaten 2–1. This would be his last appearance before going on loan to League One club Gillingham, where he made his debut in a 2–1 away win against Doncaster Rovers on 9 September 2006. His loan with Gillingham was extended for a second month, but this extended loan did not last its full spell. He returned to the Crystal Palace bench by 28 October.
For the next match, a trip to Sheffield Wednesday, Flinders made his league debut with The Eagles, while Gábor Király was dropped to the bench for a match which ended in a 3–2 defeat. This was quickly followed by a match at Loftus Road, against Queens Park Rangers, which ended in a 4–2 loss, after which he was dropped, not returning until late December.
On 20 February 2007, Flinders was sent out on loan again. He signed for Palace's rivals, Brighton & Hove Albion, after their first choice goalkeeper Michel Kuipers was injured. He made his Seagulls debut at his previous club Gillingham, a match which his new team won 1–0.
Flinders was sent out on loan again in February 2008, this time to Yeovil Town, after their first choice goalkeeper Steve Mildenhall was injured. However, despite Yeovil signing him for further month loan period, on 27 March, Championship club Blackpool signed him on loan until the end of the season as competition for first-choice keeper, Paul Rachubka. With Blackpool's next match being an away match at Crystal Palace he was not allowed to make his debut for the club until after that match. However, his loan period finished without him making an appearance for Blackpool.
In August 2008, Flinders signed for Scottish Premier League club Falkirk on loan until January 2009, and he returned to Palace at the end of this spell. Flinders was released by Crystal Palace on 6 May 2009.
On 26 June 2009, Flinders signed for League One club Hartlepool United. He played every minute of the 2009–10 for Hartlepool in both league and cup, the next season he was limited to 26 league appearances due to an injury in mid-September which ruled him out until February which saw Pools boss Mick Wadsworth draft in Blackburn Rovers goalkeeper Jake Kean on loan to cover for Flinders.
Flinders became the first ever goalkeeper to score a goal from open play for Hartlepool when his 94th-minute header against Bournemouth on 30 April 2011 gained a point for his employers on the last home match of the season. He nearly scored in consecutive home matches for the club when against Walsall on 13 August 2011, when his 5th minute clearance from 70 yards bounced over Saddlers' keeper Jimmy Walker only for striker Colin Nish to tap in on the line for Nish's first Hartlepool goal.
Flinders signed a new contract with the club in May 2011. Flinders was nominated for League One's Player of the Month for September 2011, along with Hartlepool manager Mick Wadsworth being nominated for Manager of the Month, after conceding only two goals in four matches which saw his team win all four matches. However, he was unsuccessful as Preston North End striker Neil Mellor won the accolade.
In January 2013, Hartlepool manager John Hughes revealed to the Hartlepool Mail that club in the higher divisions were looking to sign Flinders with Hughes saying "I know there are a lot of clubs looking at big Scotty. It's no surprise others are looking at him and we're just grateful and thankful that he's in goal for Hartlepool. The way he conducts himself in his training and preparation and his values are first class."
On April 2013, prior to Hartlepool's final home match of the season, Flinders was voted Player's Player, Supporter's Player and Away Player of the Year for the 2012–13 campaign. Twelve days later, it was announced that Flinders had won the Hartlepool Mail SportsMail Player of the Year Award.
After a 0–0 draw against Portsmouth in December 2013, Flinders broke a club record for the most clean sheets in the league for Hartlepool.
Flinders became the first ever Hartlepool goalkeeper to make 200 Football League appearances for the club after a 4–0 win against Bristol Rovers in March 2014.
On 23 June 2015, Flinders signed for Hartlepool's League Two rivals York City on a one-year contract, with the option of a further year. He made his debut in the opening match of 2015–16, a 3–0 defeat away to Wycombe Wanderers on 8 August 2015. He made 48 appearances in 2015–16, as York were relegated into the National League with a 24th-place finish in League Two. York had the second-poorest defensive record with 87 goals conceded; however, Dave Flett of The Press defended Flinders, arguing that "without his saves, the club would have collected even fewer points". York exercised their option to extend his contract for 2016–17.
On 23 August 2016, Flinders was suspended for five matches by the Football Association (FA) after being found guilty of racial abuse during a match against AFC Wimbledon on 19 March 2016. He was also fined £1,250 and ordered to attend an education course. Flinders was swiftly suspended by York, being told to stay away from the club completely. In September 2016, the suspension was lifted by the club and Flinders returned to training, although he had lost his place in the team to new signing Kyle Letheren. Shortly after, Flinders was found guilty of racial abuse by the FA regulatory commission, having told AFC Wimbledon player Lyle Taylor that his wife "doesn't like your kind", after grabbing Flinders' testicles and goading him.
On 20 September 2016, Flinders joined York's National League rivals Macclesfield Town on a 28-day loan until 18 October. He made his debut four days later when starting their 2–1 away win over Guiseley, finishing the loan with five appearances. Macclesfield wanted to extend his loan, but did not have the funds to do so. Flinders again lost his place in the York team in November 2016, and left the club by mutual consent on 5 January 2017.
On 6 January 2017, Flinders signed for Macclesfield Town permanently on a contract until the end of 2016–17. He was released at the end of 2016–17.
On 31 August 2017, Flinders signed for League Two club Cheltenham Town.
Flinders made his debut for the England national under-20 team in a 3–0 win over South Korea on 6 June 2005. He finished his under-20 career with five caps, all earned in 2005.
Flinders is married with one son.As of match played 12 September 2017