Even Digimon can be trained in the art of ninjutsu.
- Kirino and her village from Ai Kora. Kirino herself doesn't exactly hide the fact she's a ninja, but she doesn't announce it to the world, either. She's another subversion of the ninja attire stereotypes, in that she wears ninja clothes in her village, and context-appropriate clothes everywhere else.
- The two main families of the anime Basilisk are all very competent ninja with unique skills that range from cool to plain freaky. Its story is often summarized as "Romeo and Juliet, with ninjas".
- Azumi, she is from a group of assasins but a lot of ninjas appear too.
- Bakugan: Shun is a ninja-in-training, being trained by his grandfather.
- Bleach: The Onmitsukido is an entire organization of ninja comprised of several families who serve the Shihouin Clan. Yoruichi was the 22nd head of her family and the first woman in its history to become head of the Keigun (lit. "Punishment Squad"). When she and her friend, Kisuke Urahara, defected from Soul Society, she was succeeded by her protege, Sui-Feng, as both head of the Keigun and as captain of the Gotei's 2nd division. Making her the first member in the Feng Clan's history to ever attain a position of power; in addition to being the second woman to ever hold both titles.
- Shura Kirigakure from Blue Exorcist is the descendant of an ancient clan of female ninjas. Her ancestor Tatsuko was a member of the Iga clan before going out on her own.
- Brave10 is a fantasy manga/anime series drawn by Kairi Shimotsuki which centers around the Ten Braves of Sanada Yukimura. The tagline for the series is 'stylish ninja action' and boy there are a lot of ninjas in a lot of unique styles getting a lot of action.
- Change 123, in its later volumes, introduces an all-female ninja clan whose members infiltrate into Motoko's school to recruit Motoko (or, rather, to recruit her alternate badass personalities). Unlike typical Highly Visible Ninjas, they actually blend into the normal world, wear plain clothes (even when they're in their ninja village), and use weapons which are disguised as normal everyday objects. Also, the words "ninja" and "shinobi" are mostly avoided. Instead, they talk about "our clan/family", "our business", "family business" and similar.
- Digimon has a number of ninja-inspired monsters.
- Two notable examples are Ninjamon and Kougamon, his Palette Swap. It should be noted, in Japan, he and Kougamon both take their names from regions and styles associated strong with the ninja arts. Other examples include:
- Falcomon from Digimon Data Squad, who's a rather straight example of this trope, along with his evolutionary stages. His Champion form, Peckmon, is a Ninja Ostrich.
- Digimon Adventure 02 has Shurimon.
- Monitormon from Digimon Fusion, which beats out all other examples in ridiculous by being ninjas with televisions for heads.
- Finally, there's several digimon conflated with ninja in the american version, but these are more straight-up samurai.
- From the Red Ribbon arc from Dragon Ball we have Purple (what title he has depends on whether your watching the original or the dubbed version). He doesn't have any true powers, but he pulls a lot of classic ninja tricks including doppelgangers (Cardboard) invisibility (hiding under water with a straw to breathe) ... er ... he's not very good at it, okay?
- Gintama is another example of the Highly-Visible Ninja variety. It has Ayame Sarutobi using her ninja skills for stalking of all things.
- In Girls und Panzer, the girls of Hippo Team are mentioned as having taken ninjutsu as an elective before the start of the series and they get some mileage out of that training in their sensha-do matches. Taking advantage of their StuG III's low profile, they regularly engage in ambush tactics and camo to score some impressive kills; using their ill-placed sashimonos to great advantage against St. Gloriana in their practice match, burying themselves in the snow to get a kill on Pravda's flag tank in their match and using ninja camouflage blankets in the film twice in the theme park to great effect.
- The manga Hanzo no Mon (titled Path of the Assassin in the Dark Horse translation) subverts the stereotypes regarding ninja attire; although Hanzo (and his wife) are ninja (usually called suppa), they wear light armor on the battlefield and the stereotypical ninja outfits when they need not to be seen at all, but otherwise wear context-appropriate clothing and act accordingly. Likewise, certain ninja have notoriety and may even appear openly when a lord holds court. In fact, Hanzo, his wife and Hanzo's ninja relatives have their wedding ceremony in normal noble/samurai clothing! (After she demonstrates her abilities as a ninja wearing "the" outfit.)
- Himawari!! and its sequel series are all about the ninja. Most of the ninja in the series actually are fairly stealthy. The heroine herself...not so much.
- The Akane Class in In the Heart of Kunoichi Tsubaki is an all-female clan of ninja.
- Igano Kabamaru is about a young boy who was raised by his grandfather to be a strong-as-iron Ninja after his parents died. At Kin'gyoku, he's one of the most amazing students that's ever attended, which interests the Student Council President to use him for his own agenda.
- One of the antagonists in Katanagatari is the Maniwa Corps, which is filled with ninja that rival Naruto in the visibility department.
- While her character class/subclass is specifically an assassin and Stealth Expert, Badass Adorable Akatsuki from Log Horizon combines her talents with ninja prowess and defines herself as such.
- Ninja are one of the major types of opponents faced by Ogami Itto of Lone Wolf and Cub. They're depicted very realistically, between the Kurokuwa ninja, spies and assassins of the shogunate, and the "Grass" ninja, who functions as extreme deep-cover agents and spies. Masters of disguise and employing all manner of "dirty" tricks imaginable, ranging from poison to psychological warfare, ninja provide Ogami's greatest challenges in the first half of the series. By the finale, after the Kurokuwa have all been lost in failed assassination attempts on Ogami, Retsudo calls in the Grass for one last desperate attempt. When all is said and done, Ogami has managed to kill his way through every ninja in Japan.
- Maken-ki!: In chapter 33, Haruko explains that the Amado family has served the Rokouju's for generations as their private oniwaban. Yuuka, in particular, is the treasurer of Tenbi's student council and doubles as their advanced scout.
- Mazinger Z: Blazas S1 and S2, two way-smaller-than-usual Robeasts Big Bad Dr. Hell built for a sabotaging mission. He especifically stated that they were ninjas. Although not very stealthy (three-meter-tall, blue-and-yellow Mechanical Beasts tend to stand out
◊), they played the part, leaping around over walls and from branch to branch, throwing shuriken and infiltrating into the enemy base. - Ryuusei no Rockman (a.k.a. Mega Man Star Force) has an entire episode devoted to Ninja. Highly-Visible Ninja with all the typical tricks. Though, the guy teaching the main cast the tricks of the trade is damn good at it. They add -de osaru on the end of every one of their sentences...and apparently, the art of ninjutsu was developed by people from the ancient civilization of Mu. One of the Ooparts is a Shuriken, and Mega Man can take on the form of a ninja... of wood.
- Almost assuredly parodied in Mobile Fighter G Gundam. Midway through the story a German ninja is introduced and takes on the role of surrogate mentor to the protagonist, Domon. He even practices German Ninjutsu. Hilariously enough, he shuns the traditional garb of a ninja and dresses in clothes that are not remotely useful in maintaining stealth. Most absurd is the mask he wears. While it does obscure his features, it is painted in the bright, primary colors of the German flag and sports a jester hat-like protrusion. That doubles as a shuriken.
- While he looks ridiculous, Schwartz is otherwise a straight example of a ninja. He's also extremely badass, able to fight on roughly the same level as Master Asia.
- Akira from My-HiME and My-Otome uses a lot of classic ninja tricks and tools, including shuriken, kunai and smoke bombs. She also uses the title "Secret Ninja", while fighting in disguise (which doesn't fool anybody). Curiously, sometimes she's seen interacting with other shadowy kuroko-wearers, implying that she indeed is a genuine ninja from a genuine ninja clan, even though that never becomes a major plot-point.
- Nabari no Ou takes place in a ninja world called Nabari which are full of modern day ninja.
- Almost everybody in Naruto. Not remotely stealthy about it, either, though they are pretty tricky with things like duplication, illusions, and replacing yourself with A LOG.
- 'Ninja' in this series seems to simply refer to those who use ninjutsu skills. The ANBU black ops division would be the local equivalent to ninja, as a group of elite warriors who are assassination experts.
- As is the Animesque counterpart Shuriken School.
- Negima! Magister Negi Magi has Kaede. While she doesn't necessarily stick out like a sore thumb, she isn't very concerned with stealth either. Wields a big friggin' shuriken that from tip-to-tip is taller than she is. And that's saying something.
- The ninja in Ninja Nonsense are incompetent ninja who usually don't even carry shuriken; when they all suddenly produce shuriken and every one hits its target, causing another character to think that maybe they are skilled after all, one calls his mother on a cell phone to tell her that he has touched a shuriken for the first time.
- Nobuo Matsuri of Ninja Papa is a retired ninja. Or he would be if he weren't forced to bust out his deadly skills at least once a chapter.
- Ninja Slayer is the story of a man who becomes a ninja so he can slay all evil ninjas. That said, in this setting, most ninjas are more than just assassins; they have to fuse with the soul of a dead ninja (which on-screen only happens when the recipient is at the brink of death) which then gives them superhuman powers, and they're frequently equipped with high-tech gear such as Power Armor.
- Ninku: The heroes are all Ninjas who face off against some former Ninja as well as practitioners of other ethereal martial arts such as Feng Shui users. The Ninku gain their powers by drawing on the power of the elements themselves which take the form of a dragon. This means they aren't constrained to chi or chakra or some finite internal reserves.
- Surprisingly, a Long Running series like One Piece has had several warrior archetypes, such as knights, samurai, and even Roman-style gladiators, but a common one such as ninja rarely appear.
- First, there's Binz, one of the Co-Dragons from the movie Film Z. Yes, that's a Non-Serial Movie villain.
- On the cover page of Chapter 766,◊ there's a character behind Nami that is heavily implied to be Naruto himselfnote .
- When Kanjuro the samurai speaks about his comrade named Raizo in Chapter 803 and mentions that he's a ninja, all of the guys are amazed, complete with gleaming lights above them (including Law). It's as though they're anticipating the first canonical Ninja of the entire series.
- One-Punch Man has Speed-of-Sound Sonic, who, as his name makes redundantly clear, can move at the speed of sound, and is an all around capable enough fighter to be a match for some S-class heroes. Unfortunately for him, his appearances mostly end with him being thoroughly thrashed by Saitama.
- Later chapters reveal that there is an entire village dedicated to training children into Ninja who sell their services, and the S-Class hero Flashy Flash as well as Sonic were products of this village. It is run by a Mysterious Leader, who is built up to be light-years ahead of Sonic and Flash in skill...and gets off-screened by Saitama.
- Yamazaki Susumu is one of the two ninja who appear in Peacemaker Kurogane.
- Like their game counterparts, Koga and his daughter Janine in Pokémon Adventures are modeled after stereotypical ninja, but the author obviously had some fun making their techniques even more ninja-esque, such as outfitting their Pokeballs into shuriken. At one point, Janine even uses hand seals, presumably as signals to command her Grimer without having to actually say anything out loud.
- The Canon Foreigner Sasuke Sarugakure in Ranma ½ subverts the character type by being borderline incompetent (he's clumsy and has virtually no combat capabilities, but is a master of stealth and can move too fast to be seen) in a neighborhood filled with world-class non-ninja martial artists. In the manga, Wholesome Crossdresser Konatsu plays it a little more straight. Ukyō Kuonji uses a spoof style that merges archetypical ninja moves with cooking tools.
- Rurouni Kenshin has the Oniwabanshuu, a group of onmitsu that are initially opponents to Kenshin under the leadership of Shinomori Aoshi. When Kenshin travels to Kyoto to fight Shishio Makoto, they become allies. They are a somewhat more realistic interpretation, being inspired by the real thing.
- Saint Seiya Omega has Wolf Haruto, a descendant of a clan of shinobi who mixes his ninja fighting style with Saint techniques. So, he both is a Ninja and a Saint of Athena.
- The OVA version of Sakura Wars slyly acknowledges the origin of the traditional ninja garb — The stage crew of the Imperial Theatre — the secret headquarters of the Flower Division — are all ninja, and ninja with all manner of "ninja magic" at that.
- Samurai Deeper Kyo has many ninjas on both Kyo's and the Mibu clan's side. Sanada Yukimura has the Jyuuyuushi (The Ten Sanada Brave) which includes Sarutobi Sasuke and Kirigakure Saizo. Fuuma Kotaro is Sasuke's childhood friend, who is also one of the Jyuunishinnsho (The Twelve Heavenly Gods) and believes Sasuke had betrayed him.
- In Shy, there exist multiple ninja villages in rural Japan detached from the outside world. Their goal is to protect the world from the shadows against potential threats.
- Sonic X has Espio the Chameleon. He is (unlike the others in his group) calm and collected. As a part of the Chaotix detective agency, he made his debut in episode 39 (a loose tie-in with the game Sonic Heroes). That was, however, his only appearance on Earth. In fact, that was his ONLY appearance in the original 52 episodes! He would later go on to appear in episode 59, where he is again seen with the Chaotix crew. During season 3 he became more of a prominent character. The appearances of the Chaotix were strictly for filler episodes until episode 74, where they became background characters for each of the remaining episodes, participating in combat against the Metarex. Akin to his video game counterpart, Espio uses all manner of Ninja skills to battle opponents. His trademark ability is to turn invisible to sneak up on his enemies. He also uses a variety of weapons including an enormous collection of shuriken, and even threatens Sonic's life at one point with one of his kunai ninja knives.
- Soul Eater's Black Star and Tsubaki. Black☆Star is your typical Highly Visible variety, and somehow manages to make a big deal of being 'stealthy' even when he bothers to try. Tsubaki is a member of a clan of ninja-associated Living Weapons (kunai, (big) shuriken, smoke-bomb, camouflage, katana, chain-scythe) and frequently has to remind her meister how he should be behaving. Such as the fact that telling your target you're here to assassinate them is a bad idea.
- One two-part episode of Speed Racer featured ninjas who drove ninja racecars. Since American audiences at the time had not yet heard of ninja, the dub for American TV called them "assassins".
- Symphogear: Shinji Ogawa, who is Tsubasa's manager, is a ninja who uses guns instead of traditional ninja weaponry and he wears a business suit all the time rather than having the typical attire. Throughout the course of the series, with more seasons coming up, he demonstrates multiple crazy skills without having a Symphogear, such as running on water, changing the trajectory of his bullet that can Shadow Pin the enemy (a technique he taught Tsubasa), or creating shadow clones with his car. In X-Drive Unlimited, we get to see more of his ninja techniques, e.g. summoning a giant toad in the opening.
- In Transformers: ★Headmasters, Sixshot is presented as one of these. Subsequent series would feature Sixknight and Greatshot, who were all members of the same secret order of ninja six-changers as Sixshot, called the Six Clan.
- In the Japanese version of Transformers: Robots in Disguise, the Spy Changers are portrayed as ninjas.
- Under Ninja is set in an Alternate History world where ninja existed as an actual secret organization under the control of the Japanese government, and have continued to do so into the modern-day era. Unfortunately, in a post-Cold War Japan their services are at an all-time low in demand, leading to thousands of unemployed ninja living in Japan competing for vanishingly few ninja jobs while otherwise trying to blend into Japanese society.
- Variable Geo: Chiho Masuda is a ninja waitress, in service to a shadow organization that has secretly monitored the events of the VG tournament since its inception. She enters the competition under orders to investigate The Jahana Group's activtities in order to find evidence of their corruption and expose them.
- Sagiri from Yuuna and the Haunted Hot Springs, is part of the Ameno clan, who are Demon Slaying Ninjas.
