| — | This Is MST 3K | Self |
| 2024 | Doctor Who | The Toymaker |
| 2024 | Doctor Who: Unleashed | Self |
| 2024 | Dolly Parton's Pet Gala | |
| 2024 | Group Therapy | |
| 2023 | Drag Me to Dinner | Self - Judge |
| 2023 | Doctor Who: 60th Anniversary Specials | The Toymaker (archive footage) |
| 2023 | Billion Dollar Babies: The True Story of the Cabbage Patch Kids | Narrator (voice) |
| 2023 | Handsome Podcast | Self |
| 2022 | The Unbearable Weight of Massive Talent | Richard Fink |
| 2022 | How I Met Your Father | Barney Stinson |
| 2022 | Uncoupled | Michael Lawson |
| 2022 | Elton John Live: Farewell from Dodger Stadium | Self |
| 2021 | The Matrix Resurrections | The Analyst |
| 2021 | 8-Bit Christmas | Adult Jake Doyle / Narrator |
| 2021 | It's a Sin | Henry Coltrane |
| 2021 | Coded: The Hidden Love of J.C. Leyendecker | J.C. Leyendecker (voice) |
| 2020 | Get Organized with The Home Edit | |
| 2020 | Home Movie: The Princess Bride | Westley |
| 2020 | Visible: Out on Television | Self - Narrator (voice) |
| 2020 | Take Me to the World: A Sondheim 90th Birthday Celebration | Self - Performer |
| 2019 | The Kelly Clarkson Show | Self |
| 2019 | Dads | Self |
| 2019 | Still Laugh-In: The Stars Celebrate | |
| 2019 | Wig | Self |
| 2019 | Star Wars: Galaxy's Edge - Adventure Awaits | Self - Host |
| 2019 | Epcot International Festival of the Holidays – Candlelight Processional | Narrator |
| 2018 | Elton John: I'm Still Standing - A Grammy Salute | Self |
| 2018 | Mickey’s 90th Spectacular | Self |
| 2018 | Genius Junior | Host |
| 2017 | Downsizing | Jeff Lonowski |
| 2017 | A Series of Unfortunate Events | Count Olaf |
| 2017 | Carpool Karaoke: The Series | Self |
| 2017 | Mystery Science Theater 3000 | Neville LaRoy |
| 2017 | The Words That Built America | Self - Reader - Declaration of Independence |
| 2016 | Neil Patrick Harris: Circus Awesomeus | Host / Himself |
| 2015 | Lip Sync Battle | Himself |
| 2015 | Hot Ones | Self |
| 2015 | Best Time Ever with Neil Patrick Harris | Himself |
| 2015 | In Their Own Words: Jim Henson | Self - Actor |
| 2014 | Gone Girl | Desi Collings |
| 2014 | A Million Ways to Die in the West | Foy |
| 2014 | The Tonight Show Starring Jimmy Fallon | Self |
| 2014 | Late Night with Seth Meyers | Self |
| 2014 | Steve's First Bath | Steve (voice) |
| 2014 | Attack of the 50-foot Gummi Bear | Steve the Monkey (voice) |
| 2014 | Off Camera with Sam Jones | Self |
| 2014 | 73 Questions | Self |
| 2013 | Cloudy with a Chance of Meatballs 2 | Steve (voice) |
| 2013 | The Smurfs 2 | Patrick Winslow |
| 2013 | The Out List | Himself |
| 2013 | Beat Bobby Flay | Self |
| 2013 | Stephen Fry: Out There | Himself |
| 2013 | Disney Parks Christmas Day Parade | Host |
| 2012 | American Reunion | Celebrity Dance-Off Host |
| 2012 | Robot Chicken: DC Comics Special | Two-Face / Black Manta (voice) |
| 2012 | Finding Your Roots | Self |
| 2012 | The Penguins of Madagascar: Operation Blowhole | Dr. Blowhole (voice) |
| 2012 | Neil's Puppet Dreams | Neil Patrick Harris |
| 2012 | A Snow White Christmas: Opening Night | The Magic Mirror |
| 2011 | American Horror Story | Chester Creb |
| 2011 | The Smurfs | Patrick Winslow |
| 2011 | Beastly | Will Fratalli |
| 2011 | The Muppets | Neil Patrick Harris |
| 2011 | A Very Harold & Kumar Christmas | Neil Patrick Harris |
| 2011 | Brain Games | Himself - Host |
| 2011 | Company | Robert |
| 2011 | Billy on the Street | Self |
| 2011 | Hamish and Andy's Gap Year | Self |
| 2010 | Adventure Time | Prince Gumball |
| 2010 | Batman: Under the Red Hood | Dick Grayson / Nightwing (voice) |
| 2010 | Cats & Dogs: The Revenge of Kitty Galore | Lou (voice) |
| 2010 | Conan | Self |
| 2010 | The Best and the Brightest | Jeff |
| 2010 | A First Look at Batman: Under the Red Hood | Self |
| 2010 | Dracula's Daughter vs. the Space Brains | Dan |
| 2010 | Sesame Street: 40 Years of Sunny Days | The Shoe Fairy (uncredited) (archive footage) |
| 2010 | Through a Dog's Eyes | Narrator |
| 2009 | Cloudy with a Chance of Meatballs | Steve (voice) |
| 2009 | Glee | Bryan Ryan |
| 2009 | RuPaul's Drag Race | Self - Judge |
| 2009 | Late Night with Jimmy Fallon | Self |
| 2009 | Watch What Happens Live with Andy Cohen | Self - Guest |
| 2009 | Yes, Virginia | Dr. Philip O'Hanlon (voice) |
| 2009 | Top Chef Masters | Himself - Guest Judge |
| 2009 | Beyond All Boundaries | 1st Lt. David Hettema / Sgt. William Manchester |
| 2008 | Harold & Kumar Escape from Guantanamo Bay | Neil Patrick Harris |
| 2008 | Dr. Horrible's Sing-Along Blog | Dr. Horrible |
| 2008 | Justice League: The New Frontier | Barry Allen / The Flash (voice) |
| 2008 | The Penguins of Madagascar | Dr. Blowhole (voice) |
| 2008 | Batman: The Brave and the Bold | Music Meister (voice) |
| 2008 | Prop 8: The Musical | A Very Smart Fellow |
| 2008 | Commentary! The Musical | |
| 2008 | Dr. Horrible's Sing-Along Blog | Doctor Horrible |
| 2008 | Million Dollar Password | |
| 2007 | The Graham Norton Show | Self |
| 2007 | The Making of Dr. Horrible's Sing-Along Blog | Himself |
| 2007 | Eloise Goes to School | |
| 2006 | Rachael Ray | |
| 2006 | The Megan Mullally Show | Self - Guest |
| 2006 | Me, Eloise | (voice) |
| 2006 | Me, Eloise | Philip (voice) |
| 2005 | How I Met Your Mother | Barney Stinson |
| 2005 | Serenity | Screaming Reaver (uncredited) |
| 2005 | Numb3rs | |
| 2005 | The Colbert Report | |
| 2005 | The Late Late Show with Craig Ferguson | Self |
| 2005 | The Christmas Blessing | Nathan Andrews |
| 2005 | Disney Heroes Volume 1 | Moyo (voice) |
| 2005 | The Reichen Show | Self - Guest |
| 2005 | The Golden Blaze | The Comic Shop Owner (voice) |
| 2004 | Harold & Kumar Go to White Castle | Neil Patrick Harris |
| 2004 | Jack & Bobby | |
| 2004 | The Tony Danza Show | Self - Guest |
| 2003 | Spider-Man: The New Animated Series | Peter Parker / Spider-Man (voice) |
| 2003 | The Ellen DeGeneres Show | Self |
| 2003 | Jimmy Kimmel Live! | |
| 2003 | Punk'd | Self |
| 2003 | Spike TV VGA Video Game Awards | |
| 2002 | Undercover Brother | Lance |
| 2002 | Boomtown | Peter Corman |
| 2002 | Death from Above: The Making of 'Starship Troopers' | Himself |
| 2002 | The Making of Sweeney Todd at the San Francisco Symphony | Self |
| 2002 | The Mesmerist | |
| 2001 | Justice League | Ray Thompson (voice) |
| 2001 | Law & Order: Criminal Intent | John Tagman |
| 2001 | The Legend of Tarzan | Moyo (voice) |
| 2001 | Sweeney Todd: The Demon Barber of Fleet Street in Concert | Tobias |
| 2001 | Summer of Camp Caprice | Jed (voice) |
| 2001 | The Wedding Dress | Travis Cleveland |
| 2000 | Big Brother | Guest |
| 2000 | Static Shock | Replay / Johnny Morrow (voice) |
| 2000 | The Next Best Thing | David |
| 2000 | As Told by Ginger | Jed (voice) |
| 2000 | Ed | Joe Baxter |
| 2000 | Son of the Beach | |
| 1999 | Family Guy | Barney Stinson (voice) |
| 1999 | Joan of Arc | The Dauphin |
| 1999 | The Early Show | Self |
| 1999 | Stark Raving Mad | Henry McNeeley |
| 1998 | Will & Grace | Bill |
| 1998 | The Proposition | Roger Martin |
| 1998 | The Christmas Wish | Will Martin |
| 1997 | Starship Troopers | Colonel Carl Jenkins |
| 1997 | The View | Self - Guest |
| 1997 | The View | Self |
| 1996 | The Daily Show | Self |
| 1995 | The Outer Limits | Howie Morrison |
| 1995 | Animal Room | Arnold Mosk |
| 1995 | The Man in the Attic | Edward Broder |
| 1995 | Legacy of Sin: The William Coit Story | William Coit |
| 1995 | My Antonia | Jimmy Burden |
| 1995 | Not Our Son | Paul Keller |
| 1994 | Touched by an Angel | Jonas |
| 1994 | Snowbound: The Jim and Jennifer Stolpa Story | Jim Stolpa |
| 1993 | Late Night with Conan O'Brien | Self - Guest |
| 1993 | Homicide: Life on the Street | |
| 1993 | Sudden Fury | Brian Hannigan |
| 1993 | For Our Children | Self |
| 1992 | Time Out: The Truth About HIV, AIDS and You | Self |
| 1992 | Capitol Critters | Max (voice) |
| 1991 | Stranger in the Family | Steve Thompson |
| 1991 | The Best of Disney: 50 Years of Magic | Self |
| 1991 | Hot Country Nights | |
| 1990 | Captain Planet and the Planeteers | |
| 1990 | Blossom | |
| 1990 | The Earth Day Special | Doogie Howser M.D. |
| 1989 | The Simpsons | Neil Patrick Harris (voice) |
| 1989 | Quantum Leap | Mike Hammond |
| 1989 | Doogie Howser, M.D. | Doogie Howser |
| 1989 | B.L. Stryker | Buder |
| 1989 | Home Fires Burning | Lonnie Tibbettes |
| 1989 | Cold Sassy Tree | Will Tweedy |
| 1988 | Clara's Heart | David Hart |
| 1988 | LIVE with Kelly and Mark | |
| 1988 | Purple People Eater | Billy Johnson |
| 1988 | Too Good to Be True | Danny Harland |
| 1985 | Larry King Live | Self |
| 1984 | Murder, She Wrote | Tommy Remsen |
| 1984 | Jeopardy! | |
| 1981 | Entertainment Tonight | Self |
| 1975 | Saturday Night Live | Self - Host |
| 1975 | Saturday Night Live | |
| 1969 | Sesame Street | |
| 1956 | Tony Awards | Self - Host |
| 1953 | The Oscars | Host |
| 1951 | Hallmark Hall of Fame | Lonnie |
