- In the X-Men animated series, the Weapon X program was responsible for Wolverine's adamantium implants and memory alterations. The program (directed by Professor Thorton and Dr. Cornelius) captured Logan, Sabretooth, Silver Fox, and Maverick and used a combination of false memory implants and brainwashing techniques in order to turn them into an elite team of mind-controlled assassins. Most of the experiments and training were administered at a secret research compound in Canada. There, Thorton and Cornelius forcibly laced Logan's skeleton with adamantium using a process developed by another scientist named Dr. Oyama. Enraged by what was done to him, Logan broke free of his restraints and rampaged his way out of the facility. During the ensuing chaos, Sabretooth, Silver Fox, and Maverick were also able to escape.
- In X-Men: Evolution, Wolverine and Sabretooth were both shown to be subjects of Weapon X with a scientist operating a lab in Canada. Omega Red later mentioned other members such as Wraith.
- Weapon X is featured in the Wolverine and the X-Men episodes "Past Discretions" and "Stolen Lives". Like in the comics, Sabretooth, Maverick, and X-23 are agents of Weapon X while the program is led by Professor Andre Thorton and Dr. Abraham Cornelius. A proposed second season would have introduced Deadpool as part of Weapon X. A flashback also shows that Wolverine and Mystique were also part of Weapon X.
- Weapon X is mentioned in the Iron Man: Armored Adventures episode "The X-Factor." Pepper Potts was talking to War Machine and Iron Man via com-link about the background of Magneto. Magneto also reveals to Annie Claremont that as a boy, the Weapon X scientists did experiments on him (which hinted a link with Magneto and Weapon X).
- Weapon X briefly appears in The Avengers: Earth's Mightiest Heroes episode "Behold...The Vision". The Weapon X guards are briefly seen fighting Vision to no avail as Vision successfully steals Weapon X's adamantium supply.