The Ninjas make their first appearance in the Adventure Time animated short, where they steal an Old Man's diamonds in broad daylight in an open field. They have not been seen in the series so far. However, they have been encountered in the second level of the game Righteous Quest and on the last level of Righteous Quest 2, before the fight with Marceline.
It is also known that Finn, Jake, and the Ice King are into ninjas, as shown in "The Chamber of Frozen Blades." However, the Ice King is more into it owning several ninja artifacts and even having a secret ninja room. It is unclear if ninjas are a race of beings, an occupation, or both. In both Righteous Quest games they are shown to have some sort of servitude to Marceline.