Keogh began his career as a trainee at Ipswich Town and Stoke City, making his professional debut on loan from the latter at Icelandic club Víkingur in 2004.

Keogh was a first-team regular for Carlisle, playing 95 times and scoring six goals in all competitions for the Cumbrians over two seasons and also a short loan spell.

[2] Having been a schoolboy in Ipswich Town's academy and a ballboy at Portman Road,[5] Keogh moved on to the Stoke City youth set-up in January 2003.

Shortly after his arrival, he was an unused substitute in a 3–0 FA Cup win against AFC Bournemouth on 28 January after the squad was hit by a virus.

"[6][7] Keogh was highly thought of at Stoke: he won the Young Player of the Year Award for the 2002–03 season and played a major role in the reserves winning the 2003–04 Pontins League Championship.

[16][17] Keogh made his debut on 3 September 2005, starting and keeping a clean sheet as Bristol City drew 0–0 at home to Colchester United.

However, the next match, in which Keogh also played 90 minutes, ended in a 7–1 defeat at Swansea City and saw manager Brian Tinnion step down.

After brief substitute appearances in defeats against Brentford on 24 September and Chesterfield on 26 October, Keogh was sent out on loan by new manager Gary Johnson to League Two side Wycombe Wanderers on 9 November 2005.

City manager Gary Johnson declined to let Wycombe extend the loan and Keogh returned to his parent club on 10 December.

[21] After his loan spell ended, Keogh finally returned to Bristol City on 10 March 2006, coming off the bench in a 1–0 win at MK Dons.

He started in the middle of defence again on 27 January, scoring City's first as they came from 2–0 down to draw 2–2 against Premier League side Middlesbrough in the FA Cup, securing a replay at Riverside Stadium.

However, the season ended in success as Bristol City were promoted to the Championship as League One runners-up and Keogh was voted the club's Young Player of the Year.

Manager Keith Downing said that he was "very pleased" with Keogh's performances, calling him a "tremendous asset" who "strengthened the defence" and formed a partnership at centre-back with Shane Duff that was as good as any in the League.

In July 2008, with Keogh out of contract at the end of the season, clubs began to show an interest in signing him, though due to his age City were entitled to compensation.

[37][39] Keogh spent time on trial with Doncaster Rovers[39] but on 20 August 2008, it was announced that he had returned to Carlisle United on a permanent transfer from Bristol City, signing a two-year contract for an undisclosed fee.

[42] After not making the matchday squad for the first three matches of the season, Keogh came off the bench in the 90th minute against Leyton Orient on 23 August after the Cumbrians had been reduced to 10 men.

[43] He was indeed an ever-present for the next six League and Cup matches, until he was sent off for the first time in his career, receiving a straight red card in a 1–0 defeat to Hereford United on 21 October.

[44] Carlisle were enduring a torrid run of form and manager John Ward feared that the club were being pulled into a relegation dogfight.

However, he then suffered an ankle ligament injury in a 2–1 win at Stockport County on 18 August,[48] which kept him out of action for over a month, missing seven League and Cup matches.

He stepped up his recovery by playing 68 minutes of a reserve match against Oldham on 23 September, impressing his manager Greg Abbott with his hard work, determination and fitness levels.

They also reached the final of the 2009–10 Football League Trophy,[55] having beaten Morecambe, Macclesfield Town, Chesterfield, Bradford City and Leeds United along the way.

[66][67] A day later, Keogh was named Derby's new captain, replacing the departed Jason Shackell,[68] who covered the role after Shaun Barker's season-long injury.

[69] Keogh was an ever-present in Derby's 2012–13 season, one of only two outfield players to play in every minute of every game in the Championship and praised the team spirit at the club as well as the management style of Nigel Clough.

[75] During the 2013–14 season, a mistake by Keogh led to Bobby Zamora scoring the winning goal in stoppage time of the Championship play-off final.

[78] Keogh was an ever-present alongside Jason Shackell at the heart of Derby's defence as the side lost out 3–2 on aggregate to Hull in the Championship playoff semi-final.

[84] On 16 January 2019, the defender netted the winning spot-kick in a 5–3 penalty shootout victory over Southampton in an FA Cup third round replay with the tie having been drawn 2–2 after extra time.

[86] On 15 May, Keogh played a key role in the winning goal against Leeds United at Elland Road as he set up Jack Marriott to score as Derby reached the playoff final.

[90] In October 2019, Derby terminated the remainder of his contract due to gross misconduct,[91] with Bennet and Lawrence receiving a six-week wage fine and being sentenced to 80 hours of community service and rehabilitation.

However, after appealing to an employment tribunal with support from the Professional Footballers' Association in January 2021, it officially ruled that Keogh had been unfairly dismissed and Derby were ordered to pay £2.3 million in compensation.

On 19 January 2021, Keogh joined Championship side Huddersfield Town (with which he previously had a loan spell back in 2007) on a contract until the end of the 2020–21 season.