| Year | Title | Role | Notes |
| 1993 | Clarissa Explains It All | Paulie | Episode: "Alter Ego" |
| 1995 | As the World Turns | Stephen Anderson | 3 episodes |
| 1996 | Aliens in the Family | Ethan | Episode: "You Don't Have a Pet to Be Popular" |
| 1998–2003 | Dawson's Creek | Dawson Leery | Main cast; 122 episodes |
| 1999 | Saturday Night Live | Himself (host) | Episode: "James Van Der Beek/Everlast" |
| 2006 | Robot Chicken | Various voices | 2 episodes |
| 2007 | Criminal Minds | Tobias Hankel / Raphael |
| Ugly Betty | Luke Carnes | Episode: "Grin and Bear It" |
| Eye of the Beast | Dan Leland | Television film |
| 2008–2009 | One Tree Hill | Adam Reese | 4 episodes |
| 2008–2013 | How I Met Your Mother | Simon Tremblay | 3 episodes |
| 2009 | Medium | Dylan Hoyt | Episode: "All in the Family" |
| The Storm | Dr. Jonathan Kirk | Miniseries; 2 episodes |
| The Forgotten | Judd Shaw | Episode: "Lucky John" |
| Taken in Broad Daylight | Anthony Steven "Tony Zappa" Wright | Television film |
| Mrs. Miracle | Seth Webster |
| 2010 | Mercy | Dr. Joe Briggs | 10 episodes |
| 2011 | Law & Order: Criminal Intent | Rex Tamlyn | Episode: "To the Boy in the Blue Knit Cap" |
| Franklin & Bash | Nathan Connor | Episode: "Bachelor Party" |
| Salem Falls | Jack St. Bride | Television film |
| 2012 | Law & Order: Special Victims Unit | Sean Albert | Episode: "Father Dearest" |
| 2012–2013 | Don't Trust the B---- in Apartment 23 | James Van Der Beek | Main cast; 26 episodes |
| 2013 | The Eric Andre Show | James Van Der Beek / Team Go! Member | Episode 2 : "James Van Der Beek / Steve-O", "Lauren Conrad / Reese Witherspoon" |
| 2014 | Friends with Better Lives | Will Stokes | Main cast; 13 episodes |
| 2015–2016 | CSI: Cyber | Elijah Mundo | Main cast; 31 episodes |
| 2017 | Carters Get Rich | Trent Zebrisky | Main cast; 2 episodes |
| What Would Diplo Do? | Diplo | Main cast; 5 episodes. Also co-creator and writer |
| Room 104 | Scott | Episode: "Pizza Boy" |
| Modern Family | Bo Johnson | Episode: "No Small Feet" |
| Drop the Mic | Himself | Episode: "James Van Der Beek vs. Randall Park / Gina Rodriguez vs. Rob Gronkowski" |
| 2017–2021 | Vampirina | Boris Hauntley (voice) | Main cast; 69 episodes |
| 2018 | Pose | Matt Bromley | Main cast; 5 episodes |
| 2019 | Dancing with the Stars | Himself | Contestant (season 28) |
| 2020 | 25 Words or Less | 6 episodes |
| Home Movie: The Princess Bride | Prince Humperdinck | Episode: "Chapter Nine: Have Fun Storming the Castle!" |
| 2024 | We Are Family | Himself | Season finale; with oldest daughter Olivia |
| The Real Full Monty | Television special |
| Walker | New Neighbor | Episode: "See You Sometime" |
| 2025 | The Masked Singer | Himself / Griffin | Contestant (season 13) |
| Overcompensating | Charlie | 2 episodes |
| 2026 | Elle | Dean Wilson | Post-production; posthumous release |
