Flanagan retained his place, playing the full 90 minutes in Liverpool's next two league matches, before being substituted for Brad Jones in the 26th minute against Blackburn Rovers after his short back-pass had led to goalkeeper Doni being sent off.
Liverpool won the match 3–2.
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.
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.
Flanagan struggled through the season with injuries and was forced to miss a significant number of matches for the under-21s.
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.
Johnson's illness, coupled with José Enrique's injury, led to Flanagan starting in the left-back position in a reshuffled defence.
Flanagan made his Merseyside derby debut, a 3–3 draw away at Everton, on 23 November in a performance that was praised by his teammate Steven Gerrard, who said that the Liverpool players gave Flanagan a round of applause when he came into the dressing room after the match.
Flanagan retained his place at left-back in the next match against Hull City and was again praised for his performance, despite the match ending in a 3–1 defeat, with manager Brendan Rodgers describing his performance as "outstanding".
Flanagan scored his first goal for Liverpool with a powerful half volley in a 5–0 win away at Tottenham Hotspur on 15 December.
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.
Flanagan did not make a single appearance for Liverpool during pre-season due to a buildup of fluid on the knee.
Initially scheduled to return to first team training in early September, on 18 September Liverpool manager Brendan Rodgers confirmed that Flanagan had undergone corrective surgery on his left knee and would miss the opening months of the season.
1993
Jonathon Patrick Flanagan (born 1 January 1993) is an English former professional footballer who played as a full-back.
Flanagan started his career with Liverpool, and later played for Burnley, Bolton Wanderers and Rangers.
2010
While still in the U18 team, Flanagan made his reserve-team debut at Hull City in March 2010.
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.
He was subsequently picked out as one of the reserve team to watch by The Times sport writer Tony Barrett.
Flanagan was awarded young player of the 2010–11 season for his consistent contribution at right-back.
He was delighted to receive this award, and said there were a number of names that helped him to progress so much.
He quoted after receiving the reward, "I would first of all like to thank the gaffer, Dalglish. He believed in me, and decided I was good enough for the starting line up, and I couldn't wish for a better manager to play under."
2011
Flanagan made his first team debut when he started the Premier League match against Manchester City at Anfield on 11 April 2011, being handed the number 38 shirt and playing at right-back.
Liverpool went on to win the match 3–0, with the 18-year-old playing the full 90 minutes.
""The young boy is not bad.
For us that is really encouraging as well because it is a reflection of the work that is being done at the academy and if we have a strong academy it can only benefit us for years to come.""
- Kenny Dalglish commenting on his debut.
Flanagan continued his spell in the first team to cover for the long-term injuries of Martin Kelly and Glen Johnson, making his second start the following weekend and playing the full match in a 1–1 draw at the Emirates Stadium against Arsenal, a match in which he accidentally knocked out stand-in captain Jamie Carragher through a clash of heads.
The incident did not faze the 18-year-old, however, as he gave an assured performance.
In the following home match, against Birmingham City and playing alongside fellow Liverpool Academy graduate Jack Robinson, Flanagan again played the full 90 minutes and helped Liverpool to keep a clean sheet in a 5–0 win.
His performance earned him a place in BBC Sport pundit Garth Crooks's Premier League team of the week.
In Flanagan's fifth start for Liverpool, he was employed as a left-back against Fulham, with Liverpool winning 5–2.
His next match, against Tottenham Hotspur, resulted in him conceding a controversial penalty for minimal contact on Spurs' Steven Pienaar.
Liverpool lost the match 2–0, thus falling out of a UEFA Europa League spot with one match left of the season.
On 8 July 2011, Flanagan signed a new long-term contract with Liverpool.
Flanagan played the full 90 minutes in Liverpool's opening Premier League match of the season at home to Sunderland, a 1–1 draw.
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.
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.
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.
2014
He played in one full international match for the England national team, in 2014.
2015
On 29 March 2015, Flanagan made his return from injury playing 30 minutes in a Liverpool All-Star charity match at Anfield.
