The origins of Shiatsu lie firmly rooted in ancient Chinese medical philosophy and practice. A series of exercises for health and sensory control, known as Tao-Yinn, where developed by Bodidharma around 530BC. Tao-Yinn included self-massage and the use of acupressure and became an integral part of health services, which where later exported to Japan, Southeast Asia and Korea. Traditional Chinese Medicine was introduced into Japan in the early centuries AD and a form of massage known as 'Anma', was practiced widely in Japan. The working principles of Anma where based on the Chinese theories of meridians and acupressure points. In the 8th century AD, Anma was officially recognised by the medical authorities. Over the centuries Anma lost its official status and popularity and it was only on the Endo period (1603 - 1868), that Anma was revived and reintroduced into medical studies. Japanese doctors of this period were required to study philosophy and practice of Anma therapy. Most lay practitioners of this period were blind, and were encouraged to develop their tactile sensitivity. By the time Western massage was introduced into Japan in the late 19th century, numerous vocational Anma schools for the blind existed all over Japan.

By the 20th Century, Anma therapy had been reduced to a form of treatment used only for treating simple muscular tension and licensed only for providing comfort to the receiver. The name Shiatsu was then coined to avoid restrictive legislation applied to Anma and to continue using the traditional approach to treatment.

By the mid 1950's, Shiatsu was acknowledged as a legitimate form of therapy by the Japanese Government.

The official recognition and revival of interest in the 20th century of Shiatsu can largely be attributed to the work of Tokujiro Namikoshi, who integrated his knowledge of Anma and western massage and opened the Shiatsu Institute of Therapy at Hokkaido. He brought Shiatsu into alignment with western medicine and concentrated on applying pressure to reflex points that relate to the central and autonomic nervous system rather than to the classical meridians. Leaving the school in charge of his students, he established the Japan Shiatsu Institute, (later to change its name to Japan Shiatsu School), in 1940. In 1964, Shiatsu was recognised as an individual form of therapy, independent from Anma and other massage techniques.

In Japan today there are two distinct forms of Shiatsu. One developed by Tokujiro Namikoshi and another developed by a former student of his, Shizuto Masunaga. The method developed by Masunaga combines Western physiology with the traditional Oriental medical teachings.

Shiatsu began to gain wide popularity in the United States, Europe and Australia in the 1970's. In Europe, the Namikoshi and the Masunaga method, (also known as Zen Shiatsu) have primarily influenced Shiatsu, as well as Macrobiotic Shiatsu, which combines Macrobiotic theory with traditional teachings.