[5] Having been called up to the first team in the 2003–04 season, Flood made his debut in the qualifying round of the 2003–04 UEFA Cup, in a 7–0 aggregate win over Total Network Solutions.

[10] On 21 September 2004, Flood was called up to City’s first team for a match against Barnsley in the Football League Cup and scored his first career goal, in a 7–1 win to help the club advance to the next round.

Local newspaper Manchester Evening News said about the player: "Flood played four matches in a row in October–November when he opened his scoring account but his form seemed to tail off and other Academy products have jumped ahead of him.

However, after struggling to settle at Ninian Park, Flood joined Scottish Premier League side Dundee United on a season-long loan for the 2007/08 season.

[45][46] He quickly established himself in the first team, playing in the midfield position, [47] and his performances were praised by manager Craig Levein, describing him as "a really good, creative player".

[50][51] In follow-up interviews the next day after winning the award, Flood said he would be disappointed to leave the club at the end of the season, admitting he would be "gutted because I have loved it here.

By the start of the 2009–10 season, with Celtic under the new management of Tony Mowbray, Flood found himself out of the first team and expressed unhappiness that he was considering leaving the club.

[78] On 13 January 2010, it was announced that Flood had left Celtic for Championship side Middlesbrough, along with his teammates Barry Robson and Chris Killen.

[4][81] On 23 January, he scored his first Boro goal in his second game against Swansea City from a cross which turned into a 35-yard shot into the top corner, in a 1–1 draw.

[87] In the opening league game of the season against Ipswich Town, however, Flood suffered a serious injury with a dislocated knee, a previous injured he sustained while at Cherry Orchard, after a collision with teammate Matthew Bates and was taken off before half time.

[93] On 16 April 2011, Flood made his first appearance since being injured, coming on as a 60th minute substitute for Andy Halliday as Middlesbrough drew 1–1 with Barnsley.

[96] Former teammate Craig Conway, who just left the club for Cardiff City, was reported to have said that Flood’s return was a "good piece of business" and the Arabs supporters will enjoy his arrival.

[99] Flood made his third debut for the club, starting the whole game, in a 1–0 loss against Śląsk Wrocław, in the first leg of the UEFA Europa League Second qualifying round.

[108] However, he was unable to help Dundee United overturn the deficit in the return leg, as the club loss 5–0, resulting in their elimination from the tournament.

[122] After the match, McInnes praised Flood’s performance, describing him as "the catalyst, energetic, passionate and dictates the tempo of the game, with and without the ball.

"[123] Having made four appearances for Aberdeen so far, however, he sustained a hamstring injury while chasing a ball, and was substituted in the 55th minute, as the club beat Alloa Athletic 6–5 in penalty shoot-out in the second round of Scottish League Cup on 27 August 2013.

"[133] In the Scottish League Cup final against Inverness Caledonian Thistle, he started the whole game for 120 minutes following a 0–0 draw and Aberdeen won 4–2 on penalties to win the tournament.

[149] Amid to his future at Aberdeen, Flood played in both legs of the UEFA Europa League first round match against CS Fola Esch, winning 3–2 on aggregate.

[157] During his fourth reign as captain in a 3–0 loss against Falkirk on 17 September 2016, he suffered a thigh injury, resulting in his substitution in the 53rd minute, and was out for three weeks.

[162] Flood played all six matches in the play–offs, as the club reached final against Hamilton Academical but Dundee United fell short, losing 1–0 on aggregate, failing to win back promotion to the Scottish Premiership.

[164] On 21 June 2017, Flood signed a contract extension with the club and aimed to help Dundee United reach promotion to Scottish Premiership once again.

[165] At the start of the 2017–18 season, Flood found his playing time, coming from the substitute bench, having recovered from an injury during Dundee United’s pre–season.

[173] In the first leg of the semi–finals play–offs against Livingston, he received a red card for a second bookable offence, in a 3–2 loss (in what turns out to be his last match in his professional football career).

[174] His suspension in the return leg saw Dundee United drew 1–1, resulting in the club failing to win promotion back to the Scottish Premiership for the second time.

[178] Following his departure from Dundee United, Flood signed a one-year contract with fellow Scottish Championship club Dunfermline Athletic on 18 June 2018.

[179] Upon joining the club, manager Allan Johnston felt the signing of Flood would benefit Dunfermline Athletic’s promotion to the Scottish Championship.

[196] His good performances resulted in Republic of Ireland U21 team manager Don Givens suggesting Flood could be the next captain for the U21 side.

[198] Flood's performance at Aberdeen caught the eye of Roy Keane, earning him a call-up to the Republic of Ireland Senior squad.

[200] In June 2007, he became a first-time father when his wife Antoinette gives birth to their first child, causing his move to Dundee United put on hold for the time being.

[201][185] In December 2005, Flood's home in the Wythenshawe area of Manchester was the subject of a burglary in which he was threatened and taunted at knifepoint for over 20 minutes by a 29-year-old man.