Pein (¥Ú¥¤¥ó, Pein), is the leader of Akatsuki and a missing-nin from Amegakure, and is said to be from the Fuma clan. He is referred to as "leader" by all Akatsuki members except for Konan, who refers to him by his name. Although he directs the actions of the other members and maintains authority over them, Pein takes orders from Tobi. During Amegakure's civil war, Pein acted as the leader of the rebelling faction. He ended the conflict by singlehandedly killing the village's leader, Hanzo, as well as Hanzo's family, friends, and affiliates. In doing so Pein eliminated all who might oppose him, as well as becoming a god-like figure amongst the townspeople. He now uses the village as his base of operations for Akatsuki. Pein initially appears as nothing more than a shadowy figure with unusual eyes, having several increasingly lighter gray circles around the pupil. Pein is shown to have six bodies in total that he can switch between via a machine. Of the two bodies he has been seen in, the only consistent physical characteristics are a large number of face-piercings and his unique eyes. He implies that each of the bodies have a specific purpose, as he switches to a different body solely to kill an intruder. Its also shown that he has had a connection with Jiraiya, calling him Jiraiya-Sensei and saying his name brings back memories, but that he no longer feels an attachment to him.

Although he has not been seen in battle, Konan states that Pein has never lost a fight. The only named ability he is seen using, the Shapeshifting Technique (ÏóÜž¤ÎÐg, Sh¨­ten no Jutsu), allows him to clone his subordinates using human sacrifices that they control and can use to engage enemies without risking their own lives. The clones formed are perfect copies of the original, possessing any unique genetic traits or weapons they may possess. The clone's abilities are proportionate to the amount of chakra, a form of energy required for combat in Naruto, given to the clone. Pein has also displayed the ability to detect the movements and chakra levels of people traveling within rain, as well as the ability to control rain, such as stopping it or keeping it going for long periods of time.