Actor
- Toussaint (2010) ....
- Mary Mother of Christ (2010) .... Gabriel / Lucifer
- From Paris with Love (2010) .... James Reece / Richard Stevens
- The 66th Annual Golden Globe Awards (2009) .... Himself
- Sexo en serie (2008) .... Himself (also archive footage)
- The Children of Huang Shi (2008) .... George Hogg
- 5th Annual Irish Film & Television Awards (2008) .... Himself
- Reinventando Hollywood (2008) .... Himself (archive footage)
- August Rush (2007) .... Louis Connelly
- The Tudors: Royal Stylemakers (2007) .... Himself
- The Tudors (2007) .... King Henry VIII (22 episodes, 2007-2009)
- Mission: Impossible III (2006) .... Declan
- 50 premios Sant Jordi de cinematografía (2006) .... Chris Wilton (archive footage) (uncredited)
- Match Point (2006) .... Chris Wilton (as Jonathan Rhys Meyers)
- The Tesseract (2005) .... Sean
- Elvis (2005) .... Elvis Presley
- The Late Late Show Episode dated 20 May 2005 (2005) .... Himself
- Alexander (2004) .... Cassander
- Vanity Fair (2004) .... George Osborne
- The Lion in Winter (2004) .... Philip
- I'll Sleep When I'm Dead (2004) .... Davey
- Tracking 'The Lion in Winter' (2004) .... Himself
- Octane (2003) .... The Father
- The Emperor's Wife (2003) .... Chamberlain
- Prozac Nation (2003) .... Noah
- Bend It Like Beckham (2003) .... Joe
- Happy Now (2002) .... Mark Wraith
- The Magnificent Ambersons (2002) .... George Amberson Minafer
- Tangled (2001) .... Alan Hammond (as Jonathan Rhys-Meyers)
- Gormenghast (2000) .... Steerpike
- The Disappearance of Finbar (2000) .... Finbar Flynn
- Titus (2000) .... Chiron
- Ride with the Devil (1999) .... Pitt Mackeson
- B. Monkey (1999) .... Bruno
- The Loss of Sexual Innocence (1999) .... Nic, aged 16
- Velvet Goldmine (1998) .... Brian Slade
- The Governess (1998) .... Henry Cavendish
- The Tribe (1998) .... Adam
- The Maker (1997) .... Josh Minnell
- Telling Lies in America (1997) .... Kevin Boyle
- Samson and Delilah (1996) .... Sansone a 14 anni
- Lengua asesina, La (1996) .... Rudolph
- Michael Collins (1996) .... Collins' Assassin (as Jonathan Rhys Myers)
- A Man of No Importance (1994) .... First Young Man (as Jonathan Rhys-Myer)


