| Year | Title | Role | Notes |
| 1988 | Lip Service | Stage Manager | Television film |
| 1991 | Law & Order | Patrick Dunne | Episode: "Life Choice" |
| Shannon's Deal | Mercer | 2 episodes |
| A Woman Named Jackie | Ken O'Donnell | Miniseries |
| 1993 | The Young Indiana Jones Chronicles | Dickinson | Episode: "Princeton, February 1916" |
| 1994 | The George Carlin Show | Dad | Episode: "George Does A Bad Thing" |
| 1995 | Tyson | Kevin Rooney | Television film |
| The Commish | Tom Cannon | 2 episodes |
| Central Park West | Manager | Episode: "Behind Your Back" |
| 1996 | Touched by an Angel | Don Dudley | Episode: "Lost and Found" |
| 2000 | Sports Night | The Stranger / Calvin Trager | 2 episodes |
| Sex and the City | Harris Bragen | Episode: "Don't Ask, Don't Tell" |
| The Practice | Julie McGrath's Brother | Episode: "Brother's Keepers" |
| 2001–2004 | The West Wing | FBI Special Agent Michael Casper | 8 episodes |
| 2002 | My Sister's Keeper | Harvey | Television film |
| Live from Baghdad | Eason Jordan | Television film |
| 2003 | Will & Grace | Cam | Episode: "May Divorce Be with You" |
| 2004 | The Shield | William Faulks | 2 episodes |
| 2005 | CSI: NY | Allen McShane | Episode: "The Fall" |
| 2006 | The Road to Christmas | Tom Pullman | Television film |
| 2006–2010 | The New Adventures of Old Christine | Richard Campbell | Main role |
| 2012–2017 | Ultimate Spider-Man | Phil Coulson, Nanny Bots (voice) | Main cast; 29 episodes |
| 2013 | Comedy Bang! Bang! | Himself | Episode: "Clark Gregg Wears a Navy Blazer & White Collared Shirt" |
| 2013–2020 | Agents of S.H.I.E.L.D. | Phil Coulson / Pachakutiq / Sarge | Main role; 136 episodesAlso directed episodes: "Fun & Games" and "Missing Pieces" |
| 2015 | Agents of S.H.I.E.L.D.: Double Agent | Himself | Episode: "The Mastermind Is Revealed" |
| 2016 | Lip Sync Battle | Episode: "Clark Gregg vs. Hayley Atwell" |
| BattleBots | Episode: "The Gears Awaken" |
| Agents of S.H.I.E.L.D.: Academy | 2 episodes |
| Agents of S.H.I.E.L.D.: Slingshot | Phil Coulson | Episode: "Vendetta" |
| 2019 | SMILF | Mr. Daddy | Episode: "Single Mom is Losing Faith" |
| 2020 | The Conners | Ron | 2 episodes |
| 2021; 2024 | What If...? | Phil Coulson (voice) | 3 episodes |
| 2023 | Florida Man | Deputy Sheriff Ketcher | Miniseries; 7 episodes |
| How I Met Your Father | Nick Foster | 3 episodes |
| Painkiller | Arthur Sackler | Miniseries; 6 episodes |
| 2024 | Criminal Minds: Evolution | FBI Director Ray Madison | Recurring role |
| Will Trent | Arthur Highsmith | Episode: "Me Llamo Will Trent" |
| Snowpiercer | Admiral Anton Milius | Main role (season 4) |
| 2025 | Zero Day | Robert Lyndon | Recurring role |
