He's most famous for playing the role of NCIS Special Agent Anthony "Tony" DiNozzo on CBS television series NCIS. Weatherly is also widely recognized as Logan Cale in Dark Angel and Jason Bull in Bull.
He is also the uncle of actress Alexandra Breckenridge.
- Pier 66 (1996) as Decker Monroe
- Asteroid (1997) as Dr. Matthew Rogers
- Meet Wally Sparks (1997) as Dean Sparks
- The Last Days of Disco (1998) as Hap
- The Advanced Guard (1998) as Kevin
- Winding Roads (1999) as Mick Simons
- Cabin by the Lake (2000) as Boone
- Gun Shy (2000) as Dave Juniper
- The Specials (2000) as Verdict
- Venus And Mars (2001) as Cody Battle Vandermeer
- Trigger Happy (2001) as Bill
- The Mystery Of Natalie Wood (2004) as Robert Wagner
- Her Minor Thing (2005) as Tom Lindeman
- Charlie Valentine (2010) as Danny Valentine
- The Cosby Show (1991) as Theo's Roommate
- Loving (1992 — 1995) as Cooper Alden
- The City (1995 — 1996) as Cooper Alden
- Spy Game (1997) as James Cash
- Significant Others (1998) as Ben Chasen
- Jesse (1998) as Roy
- Charmed (1999) as Brendan Rowe
- The Crow: Stairway to Heaven (1999) as James Horton
- Grapevine (2000) as Jack Vallone
- Ally McBeal (2000) as Wayne Keeble
- Dark Angel (2000 — 2002) as Logan Cale
- JAG (2003) as Anthony "Tony" DiNozzo
- NCIS (2003 — 2016) as Anthony "Tony" DiNozzo
- Major Crimes (2012) as Thorn Woodson
- Whose Line Is It Anyway? (2014) as Himself
- Hollywood Game Night (2014) as Himself
- NCIS: New Orleans (2014) as Anthony "Tony" DiNozzo
- NCIS: Los Angeles (2015) as Anthony "Tony" DiNozzo
- Bull (2016 — Present) as Dr. Jason Bull
- Directed by Cast Member: In NCIS he directed Season 8 episode "One Last Score" and Season 10 episode "Seek".
- Romance on the Set: Was in a relationship with co-star Jessica Alba during Dark Angel, they were even engaged for a while but they ultimately ended the relationship in 2003.
- Separated-at-Birth Casting: With Robert Wagner who has appeared numerous times in NCIS as Tony's father and two do look as though they could be father and son. This could also count as a Casting Gag, as Weatherly played a younger Wagner in 2004's The Mystery of Natalie Wood.