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-Class 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, some genjutsu, and above-average taijutsu skills.

When a ninja becomes a Jōnin, they may be assigned three Genin to look over. 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.