| Year | Award | Category | Nominated work | Result |
| 2003 | Young Artist Awards | Best Performance in a Feature Film – Supporting Young Actor | The Emperor's Club | Nominated |
| 2005 | MTV Movie & TV Awards | Best Kiss | The Girl Next Door | Nominated |
| Teen Choice Awards | Choice Breakout Movie Actor | Lords of Dogtown | Nominated |
| 2007 | Dallas–Fort Worth Film Critics Association Awards | Best Actor | Into the Wild | Nominated |
| Gotham Awards | Breakthrough Actor | Nominated |
| National Board of Review Awards | Breakthrough Performance | Won |
| Alliance of Women Film Journalists Awards | Unforgettable Moment | Nominated |
| Detroit Film Critics Society Awards | Best Actor | Nominated |
| 2008 | Critics' Choice Movie Awards | Best Actor | Nominated |
| Online Film Critics Society Awards | Best Actor | Nominated |
| Screen Actors Guild Awards | Outstanding Performance by a Cast in a Motion Picture | Nominated |
| Outstanding Performance by a Male Actor in a Leading Role | Nominated |
| Teen Choice Awards | Choice Movie Actor: Drama | Nominated |
| Choice Movie Actor: Action/Adventure | Speed Racer | Nominated |
| Vancouver Film Critics Circle Awards | Best Actor | Into the Wild | Nominated |
| Houston Film Critics Society Awards | Best Actor | Nominated |
| 2009 | Critics' Choice Movie Awards | Best Acting Ensemble | Milk | Won |
| Screen Actors Guild Awards | Outstanding Performance by a Cast in a Motion Picture | Nominated |
| 2020 | Once Upon a Time in Hollywood | Nominated |