[4] Promoted to the reserve team at the start of the 2010–11 season, he first featured in the Lancashire Senior Cup triumph over Oldham Athletic.

[5] Flanagan made his first team debut when he started the Premier League match against Manchester City at Anfield on 11 April 2011,[6] being handed the number 38 shirt and playing at right-back.

[13] Flanagan played the full 90 minutes in Liverpool's opening Premier League match of the season at home to Sunderland, a 1–1 draw.

[14] Flanagan played the full 90 minutes in Liverpool's 3–1 away win against Exeter City in the League Cup, and made a late substitute appearance away to Brighton & Hove Albion in the following round of the same competition.

[15] He made his 11th Reds appearance one week after his 19th birthday, replacing Fábio Aurélio in Liverpool's 5–1 win over Oldham Athletic in the third round of the FA Cup.

[15] He returned to the team on 24 March against Wigan Athletic in the Premier League in the absence of injured duo Glen Johnson and Martin Kelly.

[15] On 19 September, Flanagan was one of the clutch of teenagers who travelled to Switzerland to play Young Boys in a Europa League group match, but he was not named in the matchday squad due to injury.

[18] On 8 November, he made his first appearance of the season in the starting XI against Anzhi Makhachkala in the Europa League, playing the full 90 minutes in Liverpool's 1–0 loss in Moscow.

[citation needed] Flanagan made his first start in the Premier League in 18 months in the club's away visit to Arsenal on 2 November, after illness forced Glen Johnson out of the squad.

[20] Johnson's illness, coupled with José Enrique's injury, led to Flanagan starting in the left-back position in a reshuffled defence.

[23] He retained his place against Cardiff City on 21 December but was replaced early in the second half by Martin Kelly due to a tight hamstring which subsequently ruled him out of Liverpool's festive fixtures.

[30] On 20 January 2016, he made his first appearance in a Liverpool matchday squad in 619 days, in a FA Cup third-round replay, coming off the bench as a 49th-minute substitute in a 3–0 victory over Exeter City.

[36] Flanagan signed a two-year contract with Scottish Premiership club Rangers, managed by his former Liverpool teammate Steven Gerrard, in June 2018.

[38] Flanagan signed for Belgian First Division A club Charleroi on 4 November 2020 on a contract until the end of the season with an option for an additional year.

[50] On 4 June 2014, Flanagan made his England senior debut, replacing Alex Oxlade-Chamberlain in the second half of a friendly against Ecuador in the United States.