Kenny’s squad reached that year's FAI Cup final, which saw Dundalk FC seal a close 2–1 victory over Bohemians.

In the 2002–2003 season, Kenny made some changes within the first-team squad and led Bohemians to a Premier Division title win, granting the side qualification for the 2003–04 UEFA Champions League first qualifying round.

Although Bohemians did not progress to the second qualifying round, Kenny’s revitalised squad celebrated a 3–0 win over FC BATE Borisov, the record-holders for the most Belarusian Premier League titles won.

His time at the club was hugely successful and he has been credited for turning a team battling against relegation in the 2004 season into one which challenged for the Premier Division title in 2005, finishing runners-up.

Kenny also guided Derry City to their first advancement in European competition in over 40 years, the last seeing Norwegian side Lyn Oslo being knocked out.

A 79th-minute header from Sean Hargan was enough to give Derry a shock win in the first leg, and Stephen O'Flynn ensured a 1–0 home victory from the penalty spot.

Kenny was delighted with the win, stating: They have won the UEFA Cup twice and only a few years ago were in the group stages of the Champions League, so this is a great night for everyone connected with Derry City.

Kenny then made a return to Derry City to manage the club for the FAI Cup final win against St. Patrick's Athletic.

In January 2007, Kenny brought in Jim O'Brien, Adam Hammill, Bobby Ryan, Jamie Harris and Stephen Glass to the club and later recruited released Falkirk striker Tam McManus.

Kenny and his coaching team led Dunfermline to the Scottish Cup Final on 24 April 2007 having defeated Rangers, Hearts, and Partick Thistle, securing a 1–0 win over Hibernian in the semi-final replay.

A 2–1 defeat at Inverness CT coupled with St Mirren's 3–2 win at Motherwell saw the Fife club relegated to the First Division, despite having previously won four league games in a row.

[14] Following his departure from Dunfermline Athletic and the exit of Derry City manager John Robertson, Kenny was strongly linked with a return to the League of Ireland club.

[16] The side ended the 2012 League of Ireland Premier Division in fourth place, three points behind closest rivals St Patrick’s Athletics.

A draw with AZ Alkmaar in the Netherlands,[24] followed by a victory over Maccabi Tel Aviv in Tallaght Stadium, were the first points earned by an Irish club in the group stage of European competition.

The club's European form had attracted interest from abroad and a consortium of American investors, backed by sports-investors PEAK6, completed a takeover in January 2018.

The club's European form had attracted interest from abroad and a consortium of American investors, backed by sports-investors PEAK6, completed a takeover in January 2018.

[31] Kenny’s team secured victories over China[32] and Bahrain[33] and a draw against Mexico in the group stage,[34] with a highly competitive semi-final ending in a 2–0 win for Brazil.

In March 2021, Ireland played two 2022 FIFA World Cup qualifiers, with a loss of 3–2 to Serbia[38] and a 1–0 home defeat at the hands of Luxembourg.

[39] On 1 September 2021, Ireland led Portugal 1–0 in their third 2022 FIFA World Cup qualifier in Estádio Algarve with two minutes to play in normal time.

[40] Next, Ireland were only able to draw 1-1 at home with Azerbaijan; a late equaliser from Shane Duffy salvaged a point for the Irish against the team ranked 117th in the world.

[50] Ireland finished their participation in 2022–23 UEFA Nations League on 27 September 2023 at home to Armenia, with Robbie Brady's penalty in additional time securing a 3-2 win.

"[64] On 16 May 2024, Kenny returned to the League of Ireland Premier Division with the club he started his coaching career at, signing a contract until the end of 2029 with St Patrick's Athletic.

[67] On 25 July 2024, Kenny took charge of his first European fixture with the club, beating Vaduz of Liechtenstein 3–1 in a UEFA Conference League tie at Richmond Park, with Jake Mulraney scoring a brace and captain Joe Redmond heading home a third goal.

[68] A 2–2 draw away to Vaduz[69] then set up a tie with Sabah of Azerbaijan, who Kenny's side beat 1–0 at Tallaght Stadium[69] before again winning 1–0 away at the Bank Respublika Arena.

[73] On 8 October 2024, Kenny claimed his first trophy as Pats manager when his second string side beat St Mochta's 2–1 in the final of the 2023–24 Leinster Senior Cup.