| Year | Title | Role | Notes |
| 1990 | Orpheus Descending | Clown | Television film |
| 1998 | Grace and Glorie | Arnold Dudley |
| 1999 | Stark Raving Mad | Mr. Putnam | Episode: "The Psychic" |
| 2000 | The District | Man in Bar | Episode: "Pilot" |
| 2000–2001 | The Practice | William Hinks | 6 episodesPrimetime Emmy Award for Outstanding Guest Actor in a Drama Series |
| 2001 | The Education of Max Bickford | Ted | Episode: "Herding Carts" |
| 2002 | Law & Order: Criminal Intent | Gerry Rankin | Episode: "Phantom" |
| The X-Files | Oliver Martin | Episode: "Sunshine Days" |
| 2003 | Without a Trace | Stuart Wesmar | Episode: "Victory for Humanity" |
| Skin | Harold Scarpelli | Episode: "Secrets & Lies" |
| Whoopi | F. Thomas Erickson | Episode: "The Fat and the Frivolous" |
| 2004 | Law & Order: Special Victims Unit | Allan Shaye | Episode: "Ritual" |
| 2005 | The Inside | Marty Manning | Episode: "Pre-Filer" |
| 2006–2010 | Lost | Ben Linus | 79 episodesPrimetime Emmy Award for Outstanding Supporting Actor in a Drama SeriesSaturn Award for Best Supporting Actor on TelevisionNominated—Golden Globe Award for Best Supporting Actor – Series, Miniseries or Television FilmNominated—Primetime Emmy Award for Outstanding Supporting Actor in a Drama Series (2007–2008, 2010)Nominated—Satellite Award for Best Supporting Actor – Series, Miniseries or Television Film (2006–2007)Nominated—Saturn Award for Best Supporting Actor on Television (2007, 2009–2011)Nominated—Teen Choice Award for Choice TV Villain |
| 2007 | Lost: Missing Pieces | 2 episodes |
| 2010 | Front Line | John Winthrop | Episode: "God In America" |
| 2011 | Parenthood | Andy Fitzgerald | Episode: "Amazing Andy and His Wonderful World of Bugs" |
| Joe: Renegades | Doctor Venom | Voice, episode: "The Anaconda Strain" |
| Generator Rex | Alpha Nanite | Voice, episode: "Ben 10/Generator Rex: Heroes United" |
| 2011–2016 | Person of Interest | Harold Finch | 103 episodes |
| 2014 | The Mystery of Matter | Narrator | Voice, 3 episodes |
| 2017–2018 | Arrow | Cayden James | 7 episodes |
| 2017 | Claws | Ted | Episode: "Ambrosia" |
| 2018 | Mozart in the Jungle | Morton Norton | 2 episodes |
| 2019 | The Name of the Rose | The Abbot | 8 episodes |
| 2019–2024 | Evil | Leland Townsend | 44 episodesNominated—Critics' Choice Super Award for Best Actor in a Horror SeriesNominated—Saturn Award for Best Supporting Actor on TelevisionNominated—Critics' Choice Television Award for Best Supporting Actor in a Drama Series (2024–2025) |
| 2023–present | My Adventures with Superman | Brainiac | Voice, 6 episodes |
| 2024 | Fallout | Wilzig | Episode: "The Target" |
| 2024–2025 | Elsbeth | Judge Milton Crawford | 5 episodes |
