[4] After a run of 23 goals in 30 games for the reserves,[7] O'Connor received his maiden call into the first team squad for a league match against Cardiff City on 12 February 2000 and remained an unused substitute during the 1–1 draw.

[8] O'Connor made his Brentford debut in a 3–2 Football League Trophy semi-final defeat at Exeter City on 15 February 2000, replacing Ívar Ingimarsson after 85 minutes.

[9] A succession of injuries meant that O'Connor had to wait until December 2000 for his first appearance of the 2000–01 season, starting in a 2–2 league draw with Wigan Athletic, before being substituted for Mark Williams on 62 minutes.

[10] O'Connor's appearance against Wigan was the first of a run in the team and he scored the first senior goal of his career in a 2–1 league win over Bristol City on 20 February 2001.

[16] After signing a new three-year contract in June 2003,[17] O'Connor appeared consistently during the 2003–04 season and kept his place in the team following the sacking of Downes and the appointment of Martin Allen as manager in March 2004.

[11] O'Connor was Martin Allen's first-choice right back for the 2005–06 season and became the club's regular penalty taker, scoring from the spot against Rochdale, Tranmere Rovers and Walsall.

[26] O'Connor made 43 appearances and scored seven goals during the 2006–07 season,[27] but his efforts to prevent Brentford suffering relegation with a bottom-place finish in League One were in vain.

[28][30] Under new manager Andy Scott, O'Connor was named captain and began the 2008–09 season as a starter,[31] but he lost his place in the team after being sent off for the only time in his career, just 14 minutes after coming on for Craig Pead in a 2–1 league win over Dagenham & Redbridge on 6 September 2008.

[32] After a period out of favour, an injury to replacement captain Adam Newton in November 2008 saw O'Connor regain the armband and he went on to form a midfield partnership with Marcus Bean.

[31] Despite missing the last 9 games of the 2008–09 season with a knee ligament injury, O'Connor made 33 appearances and scored one goal as Brentford were promoted as League Two champions.

[41] Under new manager Uwe Rösler, O'Connor began the 2011–12 season mostly as a substitute and suffered a serious ankle injury in a 1–0 FA Cup first round win over Basingstoke Town on 12 November.

[52] He returned to the first team on 16 April 2013,[53] as a substitute for Lee Hodson after 66 minutes of a pulsating 2–2 draw with Sheffield United, a game which saw Tony Craig and Clayton Donaldson sent off for Brentford.

[56] Brentford's final game of the 2012–13 season was against Doncaster Rovers at Griffin Park, with the Bees needing to win to secure automatic promotion to the Championship.

[59] Trotta crashed the spot kick against the bar and Doncaster scored a breakaway goal through James Coppinger to win 1–0 and consign Brentford to the playoffs.

[61] Brentford met Swindon Town in the semi-finals of the 2013 playoffs and trailing 1–0 in the first leg, the Bees were awarded an injury time penalty, which O'Connor converted.

[53] O'Connor returned fully fit for the 2013–14 season and once again deputised at centre back for Tony Craig in the 1–1 opening day draw with Port Vale.

[77] In December 2022, in recognition of more than a quarter of a century of service to Brentford, a room at the club's new Robert Rowan Performance Centre was named in O'Connor's honour.

[6] Owing to his Irish heritage, O'Connor's form for Brentford during the 2002–03 season saw him called up by Republic of Ireland U21 manager Don Givens for his team's 2004 European U21 Championship qualifying campaign.

[8] He made his debut in a 1–1 away draw with Georgia on 28 March 2003, coming on as a substitute for John Thompson after 81 minutes and setting up the equalising goal with a pass to Noel Hunt.

[4] He enrolled on the UEFA B Licence course in the early months of the 2014–15 season (studying alongside former teammate Alan Bennett) and gained the qualification in December 2014.

[72][81] From the beginning of the 2014–15 season, O'Connor assumed coaching responsibilities at Brentford and began working with the first team, Development Squad and academy players and staff.

[90] By 2022, his matchday role had progressed to feeding then-assistant head coach Brian Riemer with information from a position up in the stand, behind the technical area.