After winning his first 12 fights between 2009 and 2012, he beat Dougie Curran in May 2012 to take the vacant English super featherweight title.
In the semi-finals, Flanagan knocked down Derry Mathews (30–7–1, 16 KOs) in round 2, winning the fight via decision 29–27 on all scorecards.
Flanagan went on to win the prizefighter tournament in the final defeating Gary Sykes (20–2, 5 KOs) via split decision (29–28, 29–28, 28–29).
[7] Flanagan challenged WBO European lightweight champion Stephen Ormond (17–1, 8 KOs) on 14 February 2015 at the Civic Hall in Wolverhampton, United Kingdom.
Zepeda sustained what looked like a bad dislocation to his shoulder due to clash of arms and was unable to continue, retiring on his stool after round 2.
The fight was originally scheduled to take place on 13 February, but was postponed after Flanagan suffered a severe tendonitis on his left foot.
[24][25] Flanagan was set to make a third defence of his WBO lightweight title against former IBF super-featherweight champion Mzonke Fana (38–9, 16 KOs) on the undercard of Tyson Fury's cancelled July 9 rematch with Wladimir Klitschko.
Fana rallied after a fourth-round knockdown from a huge left hook but Flanagan's class ensured a third successive title defence.
A card promoted by Frank Warren which would also feature Billy Joe Saunders first title defence against Artur Akavov.
Cruz failed to become boxing's first openly gay world champion after suffering a knockout loss to Orlando Salido for the vacant WBO featherweight title in 2013.
With a successful defence, Flanagan would be on course for a future unification fight against the winner of the rematch between Anthony Crolla and Jorge Linares.
Flanagan spoke of the fight claiming Cruz is a dangerous fighter but he would be looking to retain his title via stoppage.
[34][35][36] On 12 June 2017 the WBO president Francisco Valcarcel received word that promoters Bob Arum and Frank Warren were working closely together to come to an agreement for a fight to take place between Flanagan and undefeated mandatory challenger Félix Verdejo (23–0, 15 KOs).
[37] There was a hold up in the negotiations due to Verdejo being offered $175,000, however his representatives were looking for him to earn in the region of $450,000 having to travel to Flanagan's home country to challenge for the title.
[39] On 17 July, Warren emailed Top Rank to make them aware that Flanagan had suffered a leg injury, thus postponing the fight.
[45] On 26 October 2017, the WBO confirmed that Flanagan had vacated their lightweight title in order to move up the light-welterweight division.
[46][47] On 4 January 2018, Dino Duva of Roc Nation Sports stated the fight between Flanagan and Hooker would take place on 14 April in the UK.
[48] Several sources stated the fight would take place at The O2 Arena in London, with WBO middleweight champion Billy Joe Saunders headlining the card.
[49] On 20 March, Saunders suffered a hand injury in training forcing the card to be cancelled, however that fight was quickly rescheduled for 23 June 2018 at the same arena.
[50][51][52] On 12 April, Tyson Fury announced he had signed with Flanagan's promoter, Warren and was due to fight on 9 June at the Manchester Arena.
[54] Flanagan failed to become a two-weight world champion, suffering his first loss as a professional via a split decision to Hooker, who came into the contest as the underdog.
[56][57] After the bout, Hooker announced he would enter the light-welterweight World Boxing Super Series tourney, which would commence in the fall.
The other top light-welterweights to enter the tournament were Kiryl Relikh, Anthony Yigit, Ivan Baranchyk, Ryan Martin and Josh Taylor.
[60][61] At the draft gala, the number 1 seed, Interim WBC champion Regis Prograis (22–0, 19 KO), selected to fight Flanagan in the quarter-final.
Ansah repeatedly kept hitting Flanagan during breaks, which cost him one point in the third round, and culminated in his disqualification in the fourth.
[69] On 27 August 2023, Flanagan invaded the pitch of Sheffield United following a goal by Manchester City striker Erling Haaland in a Premier League match between the two sides.