The neko ninja—lit. cat ninja—are one of three major ninja clans found in Usagi Yojimbo, the others being the mogura ninja (mole ninja) and the komori ninja (bat ninja). The neko ninja possess martial arts skills and secret techniques, such as access to explosives, beyond what the other clans have, but this is due to the neko ninja being the "normal" ninja clan, while the others have special abilities unique to them; the mogura ninja launch sneak attacks by digging through the ground, and the komori ninja can fly and launch aerial attacks.
The neko ninja are the main covert operatives of Lord Hikiji, although they report to Lord Hebi as Lord Hikiji goes to great lengths to ensure that no one can concretely connect him to his plot to overthrow the Shogun. Despite the secrecy, everyone knows who the neko ninja work for. The neko ninja's main enemy is whomever Lord Hikiji sends them after; however, they are in a bitter rivalry with the komori ninja, who are also employed by Lord Hikiji.
Early on, they only make brief appearances, usually as the odd spy listening in on conversations and massed attacks on the heroes. The first neko ninja to gain any recognition is Shingen, the kashira (leader) of the neko ninja, who attempts to steal a Muramasa sword from Lord Noriyuki, which the child lord intended as a gift to the Shogun; but the theft was foiled by Usagi who switches the sword with a piece of wood, and hid the sword on some woodcutters who were heading back to the palace.
The neko ninja played a great part in the Dragon Bellow Conspiracy, where Lord Tamakuro plans war against the Shogun and the other lords, including Lords Hikiji and Noriyuki; Shingen teams up with Usagi, Tomoe Ame, Gen and Zato-Ino to stop him. Although victorious, the neko ninja lose many lives, as well as their leader; and while their work during the Dragon Bellow Conspiracy proves how invaluable they are, they are greatly weakened, and at risk of being replaced by the komori ninja.
The neko ninja start to rebuild their ranks, and Shingen's sister, Chizu becomes the new kashira, after an altercation with Chunin (executive officer) Gunji. While Chizu is one of the best the neko ninja have, it's her second-in-command, Chunin Kagemaru, who takes the initiative to ensure the neko ninja remain the favorites of Lord Hikiji; but at the same time, he is currying favor with their employers, so that he can usurp Kashira Chizu. Eventually, after a number of failed missions, Kagemaru uses his link with Lord Hebi to overthrow Chizu; but she escapes the assassination attempt, and is now on the run.
With Chizu removed as leader, there is a power struggle in the neko ninja; Kagemaru cannot fully claim the title of kashira while Chizu is still alive, and other ninja are launching their own campaigns to overthrow him. Many of them are hoping to curry favor with Lord Hikiji, the same way Kagemaru did, and factions of the neko ninja have taken to daring missions in attempts to prove themselves, such as slaughtering a town to set up an ambush on Lord Noriyuki.
The neko and Mogura ninja were featured in an episode of the 2003 Teenage Mutant Ninja Turtles series called The Real World Part One, where Leonardo was transported to their world by a villain called Ultimate Drako.