[7] Flynn won the Scottish Premier League award for Young Player of the Month for March 2010, having scored six goals in 33 games for Falkirk.

[7] On 14 July 2011, Flynn signed for Sheffield United for an undisclosed fee on a three-year deal[8] and made his competitive club début on the first day of the 2011–12 season, starting the Football League match against Oldham Athletic.

[9] During his first season at Bramall Lane Flynn established himself as first team player despite competing with the likes of Republic of Ireland International Stephen Quinn for a place in the starting eleven.

In 2013–14 Sheffield United embarked on a memorable FA Cup campaign which culminated in them reaching the Semi-Final at Wembley in which they lost 5–3 to Hull City.

They beat West Ham at Upton Park as well as Southampton at Bramall Lane en route to the Semi Final where they met Spurs and lost narrowly 3–2 on aggregate.

On 15 January 2018, Flynn joined St Mirren on a two-and-a-half-year deal and helped the club secure the Scottish Championship title and promotion in May 2018.

[15] Flynn signed a new one-year contract in June 2020, after becoming an integral part of the Saints squad and a firm fans favourite.

The pair worked together at Oldham and has led to Flynn taking the first steps towards coaching while playing his part for a St Mirren side which secured a top 6 place in 2022–23.