Ninjas are mercenary assassins, spies, and saboteurs in feudal Japan. They practiced the art of ninjutsu which focused on numerous disciplines like spiritual refinement, unarmed combat, tactics, escaping, concealment, water training, and so on and so forth. They also equipped many different weapons and tools such as swords, staffs, sai (prongs), nunchaku (chain sticks), kusarigama (chain sickles), shuriken, kunai, etc. Ninjas were masters of disguise and they usually dressed like civilians in order to avoid suspicion.
Sarutobi Shinobu (Choujin Koukousei-tachi wa Isekai demo Yoyuu de Ikinuku you desu!) descendant of the ancient ninjas and also a ninjutsu prodigy in her own right.
Ninja Murasaki (Dragon Ball)
Junko Hattori (Demon King Daimao)
Okina (Rurouni Kenshin)
E-91 Lady Ninja (Sonic X)
The Orochi Oniwanbanshu (One Piece) are among the most elite ninjas of the Wano Country who served the Evil Shogun Kurozumi Orochi.
Raizo of the Mist (One Piece) is one of the greatest ninja masters in Wano Country
Shinobu (One Piece) is a highly skilled and experienced Kunoichi, easily defeating Hanzoemon of the Orochi Oniwanbanshu in a single attack.
Fukurokuju (One Piece) captain of the Orochi Oniwanbanshu is a grandmaster of Ninjutsu.
Speed O'Sound Sonic (One-Punch Man), the modern day ninja.
A very powerful shinobi whose abilities far exceeds that of a normal shinobi, Gabimaru the Hollow (Hell’s Paradise: Jigokuraku) is a former shinobi from Iwagakure who attained legendary status due to his supernatural feats of...
...Taijutsu, as he decimated an entire room of trained samurai...
...Ninjutsu, with his Ninpō: Fire Monk which is capable of engulfing and incinerating his opponents...
...and Kenjutsu as he killed muliple opponents.
Levi Kazama (Trinity Seven) physical and ninjutsu abilities allow her to perform superhuman feats.
Tsurigane (Toaru Kagaku no Railgun) is an extremely skilled ninja who studied at Kouga School having mastered every ninjutsu tactics including deception even to her superiors.
Ayane (Dead or Alive), the head of the Hajin Mon sect of the Mugen Tenshin Clan.
Kasumi (Dead or Alive)
The Shadow Armor allows X (Mega Man X series) to perform ninja-like movements such hanging from ceilings.
Raiden (Metal Gear)
Hanzo Hasashi/Scorpion (Mortal Kombat)
Kuai Liang/Sub-Zero (Mortal Kombat), Grandmaster of the Lin Kuei.
Genji Shimada (Overwatch)
Kurenai (Red Ninja: End of Honor) is a kunoichi skilled various ninja skills, especially her wire weapon.
Espio the Chameleon (Sonic the Hedgehog) is a master of ninjutsu.
Taki (Soulcalibur) is a kunoichi skilled in delivering unpredictable and deceptive strikes.
Strider Hiryu (Strider)
Kai Leng (Mass Effect 3)
Yuffie Kisaragi (Compilation of Final Fantasy VII)
Sheik (The Legend of Zelda)
Tae Kwon Crow/Hawkmongous (Skylanders Trap Team)
Stink Bomb (Skylanders Swap Force)
Ninja Master (Valkyrie Crusade)
Raidou (Dead or Alive) a dangerously powerful Tenjinmon Ninjutsu master, his skill is superior to even Hayate.
Ayane's mentor Genra (Dead or Alive) is a highly powerful Hajinmon Ninjutsu master.
Ninjas (Final Fantasy XIV A Realm Reborn)
Ninjas Clan (Mini Ninjas)
Hiro (Mini Ninjas) is one of the youngest of the six ninjas in his clan, only one of them, as well as the only ninja in three hundred years, to be able to control Kuji magic.
Futo (Mini Ninjas) is the second ninja to be accessed in Mini Ninjas, distinguished by his size and brute strength.
Suzume (Mini Ninjas) is a female ninja, who wields a wooden flute for a pass-time and a weapon. She was the first ninja needed to be saved in Mini Ninjas.
Shun (Mini Ninjas) is one of the six playable ninjas in Mini Ninjas, his weapon of choice is a bow. He is the second ninja needed to be saved, after Suzume.
Tora (Mini Ninjas) is a claw-wielding ninja who believes he is a tiger, and has tiger-like mannerisms that stemmed from infancy that he incorporates into his fighting. He is the third ninja needed to be saved, after Shun and Suzume.
Kunoichi (Mini Ninjas) is one of two female ninjas in Mini Ninjas, who's weapon is a naginata spear. She is the last ninja needed to be saved.
Ninja Master (Mini Ninjas) is a wise elderly ninja who found all six ninjas at very young ages, and helped them to find their unique skills and develop into proficient ninjas.