| Year | Association | Category | Title | Result | Ref. |
| 2003 | Empire Awards | Best Newcomer | 28 Days Later | Nominated | |
| 2003 | Irish Film & Television Awards | Best Actor in a Leading Role – Film | Nominated | |
| 2004 | MTV Movie & TV Awards | Best Breakthrough Performance | Nominated | |
| 2005 | Irish Film & Television Awards | Best Actor in a Supporting Role – Film | Batman Begins | Nominated | |
| Best Actor in a Leading Role – Film | Red Eye | Nominated |
| 2005 | Satellite Awards | Best Actor – Motion Picture | Breakfast on Pluto | Nominated | |
| 2006 | MTV Movie & TV Awards | Best Villain | Batman Begins | Nominated | |
| 2006 | Teen Choice Awards | Choice Movie Villain | Red Eye / Batman Begins | Nominated | |
| 2006 | Saturn Awards | Best Supporting Actor | Red Eye | Nominated | |
| 2006 | British Independent Film Awards | Best Actor in a British Independent Film | The Wind That Shakes the Barley | Nominated | |
| 2006 | GQ UK Awards | Actor of the Year | Won | |
| 2007 | Irish Film & Television Awards | Best Actor in a Leading Role – Film | Nominated | |
| Best Actor in a Leading Role – Film | Breakfast on Pluto | Won |
| 2007 | British Independent Film Awards | Best Actor in a British Independent Film | Sunshine | Nominated | |
| 2008 | Irish Film & Television Awards | Best Actor in a Leading Role – Film | Nominated | |
| 2010 | Best Actor in a Supporting Role – Film | Inception | Nominated | |
| Best Actor in a Leading Role – Film | Perrier's Bounty | Nominated |
| 2011 | Irish Times Theatre Awards | Best Actor | Misterman | Won | |
| 2012 | Drama Desk Award | Outstanding Solo Performance | Won | |
| 2012 | British Independent Film Awards | Best Supporting Actor | Broken | Nominated | |
| 2014 | Irish Times Theatre Awards | Best Actor | Ballyturk | Nominated | |
| 2014 | FIPA Awards | FIPA d'or Best Actor – Series | Peaky Blinders | Won | |
| 2015 | Irish Film & Television Awards | Best Actor in a Leading Role – Drama | Nominated | |
| 2017 | National Television Awards | Best Drama Performance | Nominated | |
| 2017 | Czech Lion Awards | Best Actor in Leading Role | Anthropoid | Nominated | |
| 2017 | Irish Film & Television Awards | Best Actor in a Leading Role – Drama | Peaky Blinders | Won | |
| 2018 | Irish Film & Television Awards | Best Actor in a Leading Role – Drama | Won | |
| 2019 | National Television Awards | Best Drama Performance | Nominated | |
| 2020 | Best Drama Performance | Won | |
| 2020 | Irish Film & Television Awards | Best Actor in a Leading Role – Drama | Nominated | |
| 2022 | National Television Awards | Best Drama Performance | Won | |
| 2023 | Consequence's Annual Report | Film Performance of the Year | Oppenheimer | Won | |
| Rolling Stone UK Awards | The Film Award | Nominated | |
| 2024 | Palm Springs International Film Festival | Desert Palm Achievement Actor Award | Won | |
| Capri Hollywood International Film Festival | Best Ensemble Cast | Won | |
| Sant Jordi Awards | Best Actor in a Foreign Film | Won | |
| 2024 | Irish Film & Television Awards | Best Actor in a Leading Role – Film | Won | |
| 2024 | People's Choice Awards | Favorite Movie Actor | Nominated | |
| Favorite Dramatic Movie Actor | Nominated |
| 2024 | AACTA Awards | Best Actor | Won | |
| 2024 | Saturn Awards | Best Actor in a Film | Nominated | |
| 2024 | Satellite Awards | Best Actor – Motion Picture | Won | |
| Best Ensemble – Motion Picture | Won |
| 2024 | AARP Movies for Grownups Awards | Best Ensemble | Nominated | |
| 2025 | Irish Film & Television Awards | Best Actor in a Leading Role – Film | Small Things Like These | Won | |