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Genin (下忍; Literally meaning "low ninja", Meaning (Viz) "junior ninja") are the lowest level of ninja and also the ones that display the most difference in power. When they become genin, ninja start to do their bit for their village's economy – being sent on missions that the village gets paid for. They are typically sent either on D-rank missions, which are almost entirely risk-free jobs of manual labour, or, rarely, on C-rank missions, which are a cut above that and begin to verge on real "ninja" work that have a very low possibility of risk to the ninja involved. When Konohagakure was short-handed on upper-level ninja because of the invasion, the village had to occasionally send genin on higher-ranked missions.

Chūnin (中忍; Literally meaning "Middle Ninja", Meaning (Viz) "Journeyman Ninja") are ninja who are qualified to guide other ninja and lead missions. Chūnin have reached a level of maturity and ability that primarily consists of leadership skills and tactical prowess. Genin who do not have the skills to become chūnin are weeded out in the chūnin exams. Some of them, like Iruka Umino, Daikoku Funeno and Suzume move on to function as Academy teachers and others, like Shikamaru Nara, serve as team leaders in charge of small teams who need to make decisions and utilise the skills of the shinobi under their command to the maximum effect. Chūnin are typically sent on C-rank or B-rank missions.

Jōnin (上忍, Jōnin; Literally meaning "High Ninja", Meaning (Viz) "Elite Ninja") are generally highly-experienced shinobi with great individual skill who serve as military captains. They are often sent on A-rank missions, and experienced jōnin may even be sent on S-rank missions (which are considered to be the greatest difficulty). It is not unusual for jōnin to go on missions alone. Jōnin are generally able to use at least two types of elemental chakra,[1] some genjutsu, and above average taijutsu skills.

It is as of yet unknown what one has to undergo to become one. It is mentioned that jōnin are appointed,[2] however there was mention of a Jōnin Exam in the anime's Kurama Clan Arc. When a ninja becomes a jōnin, they may be assigned a three-man genin team to supervise. One part of their duties is to help instruct and train these genin to become competent ninja. In Konohagakure, it is up to the jōnin to decide whether a candidate Hokage would be given the position permanently. They also have a special rank known as Jōnin Commander. Shinobi who have jōnin-level skills only in a specialised area are classified as Tokubetsu Jōnin.

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