| Year | Title | Role | Notes |
| 1998 | Four Corners | Antonio | 4 episodes |
| 1998–2006 | That '70s Show | Fez | 200 episodes |
| 2002 | Grounded for Life | Eugenio | Episode: "Mustang Lilly" |
| MADtv | Punch | Episode: "#8.7" |
| 2003 | Punk'd | Himself | 3 episodes |
| 2005 | Robot Chicken | Fez | Voice, episode: "Gold Dust Gasoline" |
| 2006–07 | Yo Momma | Host | 64 episodes; also creator and executive producer |
| 2006 | The Sopranos | Himself | Episode: "Luxury Lounge" |
| Shorty McShorts' Shorts | Nestor | Voice, episode: "Dudley and Nestor Do Nothing" |
| 2006–13 | Handy Manny | Manny Garcia | Voice, main role (97 episodes) |
| 2006 | Higglytown Heroes | Helicopter Pilot Hero | Voice, episode: "Higgly Islands" |
| 2007 | That's Our Joe | Almerià | Episode: "Padre De Joe F." |
| 2010 | Extreme Makeover: Home Edition | Himself | Episode: "The Williams Family" |
| Wizards of Waverly Place | Uncle Ernesto | Episode: "Uncle Ernesto" |
| 2011 | The Cleveland Show | Diego | Voice, episode: "How Do You Solve a Problem Like Roberta?" |
| 2011–12 | Royal Pains | Eric Kassabian | 3 episodes |
| 2011 | NTSF:SD:SUV:: | Enrique | Episode: "Piper Doesn't Live Here Anymore" |
| Figgle Chat with Fred Figglehorn | Eduardo Fresco | Episode: "FRED Interviews Eduardo Fresco" |
| 2012–13 | Suburgatory | Yoni | 2 episodes |
| 2012 | Awake | Detective Efrem Vega | 13 episodes |
| Special Agent Oso | Manny Garcia | Voice, episode: "The Manny With the Golden Bear" |
| Are You There, Chelsea? | Tommy | Episode: "Those Damn Yankees" |
| Men at Work | Eri Ricaldo | Episode: "Crazy for Milo" |
| Minuto Para Ganar | Himself | Contestant |
| 2012–13 | Raising Hope | Ricardo Montes | 4 episodes |
| 2013 | RuPaul's Drag Race (season 5) | Himself | Episode: "Drama Queens" |
| 2014–16 | From Dusk till Dawn: The Series | Don Carlos Madrigal | 23 episodes |
| 2014 | Matador | Party Guest | Uncredited; Episode: "Quid Go Pro" |
| 2015 | Minority Report | Will Blake | 10 episodes |
| 2016 | Lip Sync Battle | Himself | Episode: "Gina Rodriguez vs. Wilmer Valderrama" |
| Grey's Anatomy | Kyle Diaz | 5 episodes |
| 2016–present | NCIS | Nicholas "Nick" Torres | Series regular (season 14–present) |
| 2016–17 | The Ranch | Umberto | 4 episodes |
| 2017 | NCIS: New Orleans | Nicholas "Nick" Torres | Episode: "Pandora's Box (Part II)" |
| The Price Is Right | Himself | Episode: "Celebrity Charity Week – Day 2" |
| 2018 | Last Week Tonight with John Oliver | Bird | Episode: "Crisis in Venezuela" |
| 2020 | Gentefied | Rob | Episode: "Casimiro" |
| 2022 | Celebrity IOU | Himself | S3E07, "Wilmer Valderrama's Surprise Garage Reno", aired on December 26, 2022 |
| NCIS: Hawaiʻi | Nicholas "Nick" Torres | 2 episodes |
| 2023 | NCIS: Los Angeles | Nicholas "Nick" Torres | Crossover: "A Long Time Coming" |
| That '90s Show | Fez | 3 episodes |
| TBA | Rhona Who Lives by the River | Pablo | Voice, upcoming series |
