[2] By the 2003–04 season, he had graduated to Arsenal's under-19 team[3] and once been an unused substitute for the reserves,[4] and had played international football for Republic of Ireland under-19s, qualifying via grandparents from Sligo,[5][6] and for England under-18s.

The club's academy director felt he had "the ability to play at the highest level", and prioritised adding a "work ethic and competitiveness" to his "great technique".

[17] At the start of the 2005–06 season he became part of the Birmingham first-team squad, though manager Steve Bruce warned him that he would not easily find his way into the team.

[18] On 20 September 2005, he made his Birmingham first-team debut in the League Cup away at Scunthorpe United, as a 26th-minute substitute to replace the injured Muzzy Izzet.

Despite his dismissal, he received words of encouragement from teammates Mikael Forssell and Mario Melchiot for his performance,[18] and went on to make 25 appearances in all competitions, mainly as substitute, as Birmingham were relegated to the Championship.

[25] His last match before he returned to Birmingham was an influential performance as Oldham beat Leeds United 3–1 to become the first team that season to win a League game at Elland Road.

[26][27] On 4 January 2008 Kilkenny signed for League One team Leeds United on an emergency loan, with a view to ensuring his availability for the next day's game prior to completing a permanent transfer the following week.

[28] He made his debut in the 3–0 win over Northampton Town, putting in an impressive performance to get the man of the match award.

[33] After a period out of the team and the sacking of Gary McAllister Kilkenny regained a spot in the Leeds midfield under the stewardship of new manager Simon Grayson late in the 2008–09 season.

[35] Kilkenny was part of the Leeds team who were knocked out of the play-off semi-final by Millwall; he injured an ankle and was substituted in the first half of the second leg at Elland Road.

[37] After again missing pre-season, this time because of ankle trouble, Kilkenny found himself trying to regain fitness and a place on the bench once the season was in full flow.

[39] He scored his first goal of the season for Leeds in the 3–1 win against Grimsby Town in the Trophy, "[playing] a give-and-go with Jermaine Beckford before tucking the ball into the far corner".

[45] He missed the cup replay through injury, and returned to the bench against Carlisle United in the Football League Trophy Northern Final second leg.

[citation needed] Kilkenny scored his first goal of the 2010–11 season with a penalty in the League Cup match against Lincoln City.

[57] In January he repeated his desire to stay with Leeds,[58] He returned from international duty to be named on the bench against Hull City.

[63] Kilkenny said that despite speculation linking him with a move to the Australian A-League, he wanted "to play at the highest level and that's in Europe".

[66] Ahead of his return to Elland Road with Bristol City on 17 September, he told the Yorkshire Evening Post he had never wanted to leave the club,[67] and in response to Leeds' chairman Ken Bates' comment that "Kilkenny wanted to leave for a big club and ended up at Bristol City", he felt that Bates "has always got something to say and sometimes he needs to keep quiet.

[71] Kilkenny played the whole match as Preston beat Swindon Town in the 2015 League One play-off final to gain promotion to the Championship.

He was among a group of young players, selected by manager Guus Hiddink, who trained with the Australian squad in Germany prior to the tournament, and made his international debut on 7 June 2006, coming on as a late substitute in their 3–1 victory in a World Cup warm-up game against Liechtenstein in Ulm, Germany.

Kilkenny is himself a fan of his former side Arsenal but holds an affinity with Leeds United, the team he made the majority of his career appearances with.