Chakra (チャクラ, chakura?) is essential to even the most basic technique; it is the moulding of the physical energy (身体エネルギー, shintai enerugī?) present in every cell of the body and the spiritual energy (精神エネルギー, seishin enerugī?) gained from exercise and experience. Once moulded, it can be channelled through the chakra circulatory system, which is to chakra as the regular circulatory system is to blood, to any of the 361 chakra points (called tenketsu) in the body. Through various methods, the most common of which is hand seals, the chakra can then be manipulated to create an effect that would not be possible otherwise, such as walking on water, exhaling fire or creating illusions.

By moulding different ratios of the two energies, new types of chakra can be formed. Most ninja have a natural affinity to one type of chakra, but they have the capacity to create elemental chakra apart from their own affinity. There are five basic types, each stronger and weaker to another, but their relations, weaknesses, and strengths to each other are all explored. There is also the dealing of Yin and Yang and the balance of mental and physical energies. In addition to these five elements, certain kekkei genkai can mix elemental chakra to form new natures, for example it is possible to mix water and wind into ice. While many ninja can use more than one type of chakra, very few are able to use them simultaneously.