Aikido is rooted in the medieval Japanese fighting art of Aiki-Jujitsu, which emphasized unarmed combat and the use of simple farming tools alongside traditional weapons. The secret techniques of this martial art were taught only to initiates loyal to the Minamoto clan. It was developed in the ninth century by Prince Teijun, an adept warrior and the son of the Emperor Seiwa. Prince Teijun’s technique exploited the weaknesses in his opponents body armor and was further developed by his son to emphasize depth perception between combatants.

For three centuries the prince's technique was developed and refined. It reached its peak under Saburo Yoshimitsu, a Minamoto-clan general who was also trained in anatomy. Yoshimitsu updated the techniques to have a new emphasis on the vulnerable points of the body. Yoshimitsu's son, Yoshikiyo took Aiki-Jujitsu one step further by training his soldiers in unarmed combat against swordsmen.

With the introduction of guns to Japan in the sixteenth century, like all other martial arts, Aiki-jujitsu became obsolete. Nevertheless, descendants of Yoshimitsu continued to train Aiki-Jujitsu. In the late nineteenth century, Takeda Sogaku opened a dojo to teach the art on the island of Hokkaido.

Ueshiba Morihei (1883-1969), a young martial arts student, entered Takeda's dojo in 1915. As a child Ueshiba was religiously devoted to both the Shinto sprits of his district and to the mystical Shingon Buddhist sect. He was frequently sick and suffered from a severe bout of scarlet fever. To improve his physical demeanor he took up Jujitsu, Kenjutsu and Naginata, all known for rigorous physical discipline and martial philosophy. The same factors he later rejected for a more defensive approach.

In his early years Ueshiba engaged in a number of professions, including business and agriculture. During that time he studied marital arts intensely, but was always dissatisfied with the philosophies underlying the various arts. The turning point in his life was in 1919 when he became a student of Deguchi Onisaburo, a mystic philosopher, that established a new sect incorporating the teachings of Shinto Buddism, and Taoism. Ueshiba later established a dojo to train Deeguchi's other students in the martial arts. Ueshiba later accompanied his master on a trip to Mongolia. Legend has it that upon his return to Japan, Ueshiba was taking a bath when he had a mystical vision: he saw himself, both body and mind, at one with the universe. He concluded that his training in the martial arts was the necessary link in attaining this high state of consciousness and determined its achievement should influence all his future training in the martial arts.

Influenced by the renewal of Japanese nationalism and exclusivity, Ueshiba was determined to rid the martial arts of all foreign influences, especially those of China. This culminated in the founding of a new dojo, the Kobukai, in 1931. For some years he trained military and police personnel and a select group of students. In 1938 Ueshiba's new martial art became known as Aikido.

In 1942 Ueshiba retired to a small farm that he had bought years earlier. While there, he continued to train a select group of students; although his earlier connections with Deguchi Onisaburo's alleged "revolutionary sect" made him suspect to the Japanese government. After World War II his most trusted students were sent abroad to teach harmony inspired Aikido. Ueshiba himself returned to his Kobukai dojo in 1949 and traveled to Hawaii in 1961 to demonstrate his art. He died of liver cancer in 1969 and was succeeded by his son Ueshiba Kishomaru.

Those who adhere strictly to Ueshiba's teachings, as passed on to his son, are said to practice Aikikai So Hombu. Many other of Ueshiba's students developed their own schools of Aikido, which evolved, but differed slightly, from their masters teachings. Yamada Yoshimitsu brought Aikido to the United States. Abe Tadashi taught Aikido in Europe. Tohei Koichi, who emphasized breathing technique, trained the Hawaiian police force in Aikido. Shioda Gozo, who emphasized the self-defense aspects of Aikido, trained the Toyo police force in his art of Yoshinkai. Tomiki Kenji developed a new system of self-defense, known as Yoshinkan Aikido. Unlike Ueshiba Kenji believed that competition was valuable to the attainment of spiritual advancement. He also sought ways to develop the physical aspects of Aikido into a form of aerobic exercise. Other schools that are associated with Aikido are Daito, Korindo and Yoseikan. The medicinal and resuscitative techniques, once found in Aikido are no longer in use.