In some traditions, Reiki energy is believed to enter the initiate through the 7th (crown) chakra, fill the initiate's aura and flow through her or his hands into the body of the recipient. In other traditions, it is said to enter through the 1st (root) chakra, fill the aura, become centered in the 4th (heart) chakra, and flow out through the initiate's hands. The Reiki energy is said to be "intelligent" energy, which "knows what to do", or "where it is needed". Thus, Reiki adherents say, if the recipient needs it, and is ready to heal, the Reiki energy will go where it needs to for healing. They also maintain that if, on the other hand, the intended recipient does not accept the energy on some level, the energy will not be absorbed. Some traditions teach that Reiki "spirit guides" keep watch over Reiki energy and assist the practitioner. Many teach that any intention to do harm will not facilitate the flow of Reiki energy. The doctrine is that Reiki energy is incapable of doing harm.

"Treatment" is traditionally done similarly to the laying on of hands. The clothed recipient is asked to lie down and relax. The practitioner then acts as a channel for Reiki energy, theoretically allowing the energy to be channelled through the practitioner to where the patient requires it. Usually the practitioner applies his hands to various parts of the patient's body. Some practitioners touch the body or hover their hands above it. Some patients report feeling various sensations: heat, cold, pressure, etc. Practitioners often attribute these sensations to Reiki energy filling the body and aura of the recipient and acting: filling up energy deficiencies, repairing and opening the energy channels (meridians), pulling out "negativity" and dissolving the blockages of stale energy. Others report feeling little or no change.

Reiki is purported to be a form of Oriental medicine and it defines full health as total harmony of body, mind and spirit. Some traditions label these as Body, Emotion, and Soul and are taught the technique said to be for each in that order: Reiki I, Reiki II, and Reiki III (see below).