Shinobi, also known as ninjas, are the main military force in hidden villages. A female shinobi can also be called a kunoichi. They are responsible for a large amount of the village's income through missions, in which they offer their services to contractors for money. A portion of the money goes to those taking on the mission, whilst the rest goes to the village they work for. The mission could be anything as simple as babysitting a pet, to escorting a man outside the village, to defending a point from bandits, all the way up to assassinating an enemy to the village.

Though there are many types of shinobi that specialise in different skills, all of them have at least some sort of fighting capability. They also extensively use and manipulate chakra to perform jutsu that can aid them both in and outside of a fight. Because of this, shinobi will also serve as the village's military if war breaks out, and are often seen as defenders of the village by its citizens. Shinobi are generally identified by their forehead protectors, which are marked with the symbol of the village they are from. Missing-nin are shinobi that defect from their village and are treated as traitors to be killed.