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Anime & Manga
- The Exorcists in Blue Exorcist train the students exorcists in the academy under the guise of a "Cram-Class". Which is technically true as they do do extra studies there.
- The Digidestined of Digimon Adventure 02 have referred to their group as the "Computer Club". It's basically a cover for their afterschool trips to the Digital World, using one of the school computers to get there. An early episode shows that there is a teacher who acts as the club's advisor - but he doesn't know the first thing about using computers and is a nonentity for the rest of the series. (His story purpose was to send Taichi to Not Important to This Episode Camp by forcing him to run interference.)
- In Hallelujah Overdrive: The group(s heavy metal band), masquerades as a "Experimental Physics Club" to avoid getting closed down by the principal.
- Haruhi Suzumiya: The S.O.S. Brigade is one of these with a twist. On paper, it exists to find supernatural stuff (espers, aliens and time travellers, among other things). On application, it exists only to cater to every crazy whimsy that Haruhi Suzumiya has. The 'twist' lies in that there *is* an alien, an esper and a time traveller amongst the members of the club-and their objective is to observe, report, and keep The Masquerade in front of Haruhi's eyes, because she's a Reality Warper of massive power who could bring along The End of the World as We Know It without even wanting to... and her getting bored increases the chances of it happening a whole damn lot. The Lemony Narrator and POV character of the show is the club's sole normal member, an Unfazed Everyman who is on the Dark Secret, and supports The Masquerade whole-heartedly (if snarkily).
- Negima!? has a Chupacabra-based club being used as a cover for those who discovered Negi's secret.
- Shugo Chara!: The Guardians use their Absurdly Powerful Student Council position to hunt X-Charas and fight Easter.
- The S.O.S. Brigade, in addition to its regular purpose of keeping Haruhi entertained from the source material, has a second hidden purpose in SOS Pretty Cure—specifically, it's to hide the fact that all five of them are also the eponymous magical warriors. This is most evident during the Magical Mystery Patrols.
- In Harry Potter and the Order of the Phoenix, Dumbledore's Army was formed with this intention (although they weren't keeping its purpose a secret, they weren't exactly openly advertising for members), but Umbridge got wind of it and had a rule allowing her to veto clubs introduced. As a result it became more of a secret club, the only one openly acknowledging Voldemort's return, and La Résistance in the 7th book.
- The Haunting Hour: The episode "Alien Candy" features the alien club, which is for actual aliens planning to take over the school instead of sci-fi fans, as the club advertised.
- Kamen Rider Fourze has the Kamen Rider Club at school, which is actually made up of the students helping the Kamen Riders and has a portal to a base on the moon. It is unclear just how much the club claims to be a legitimate school club - said portal is hidden in an old locker in a closed-off classroom, and they don't have a teacher sponsor until Ohsugi finds out.
- Buffy the Vampire Slayer: In the episode "Inca Mummy Girl" Buffy tells the visiting exchange student, Ampata, that she's meeting with the Archeology Club in the school library.
- In Persona 3, the Specialized Extracurricular Execution Squad (known as SEES) is registered as a school club with Chairman Ikutsuki as its advisor, and members even stay in the same dorm. However, the true purpose of the "club" is to investigate the Shadows, Tartarus and the Dark Hour, supernaturally phenomena that can only be experienced by a few. All members possess the ability to summon a Persona, which is the only known weapon against the Shadows.