The techniques in Kukishinden ryu are said to have come from China and the land beyond China. The Kukishinden ryu was developed in the Kumano prefecture.

During the life of the school it was employed by Japanese seamen to help protect them. This greatly influenced the schools techniques and weapons. Warriors of the Kukishinden ryu are said to have used masts and rigging during combat.

In 1330 the Japanese Emperor Go Daigo was held under house arrest at the Kazan-in, the Royal Summer Palace on Yoshino mountain, be the Shogun Ashikaga Takauji. It was Kusunoki Masashige, a high ranking samurai loyal to the Emperor who was ordered to effect a rescue attempt. Masashige had in his employment a young sixteen year old Gyoja (mountain ascetic) from Kishu, south of Nara, named Yasushimaru Kurando. Kurando was well known to be skilled in Ninjutsu and other Bujutsu arts and so was given the task of rescuing the Emperor.

Aided by another samurai named Kagoshima, Kurando managed to infiltrate the Kazan in, and upon reaching the emperor disguised him [the Emperor] as a woman. Unfortunately the Ashikaga samurai were alerted when Kurando attempted to croos the "Hizume corridor" with the emperor on his back. This wooden corridor was specially designed to make loud sound as was walked on, thus alerting the guards. Kurando and the emperor were surrounded, placing the Emperor with his back against a nearby tree, Kurando faced his oncoming adversaries armed with his Naginata (halberd). One by one they attacked him, and he cut them down with his Naginata, until only their samurai officer was left. This man was a highly skilled martial artist, and as Kurando cur at him with the Naginata he retaliated by cutting the blade of the Naginata cleanly away from the shaft. Now armed only with a wooden pole, Kurando defended himself and the Emperor with a secret Rokushakubo (6th staff) technique called "Gyaku Kuji". Upon defeating the samurai officer Kurando and the Emperor Go Daigo made good their escape, and then with Kagishima he escorted the Emperor back to the capital Kyoto.

In recognition for this brave act the emperor gave Kurando permission to use the "Kuki" of Kukishinden Ryu, which suggests that he fought like "Nine Demons". Although formalised at this time, the Kukishinden Ryu has a history stretching back to the Kamakura Era (1180's), with techniques that are said to originate in China and the Lands beyond.

Kukishinden ryu Hanbojutsu is the main weapon taught to students of ninjutsu in the world today and is the third school in Bujinkan.
Sensei Ueshiba the founder of modern Aikido, in his youth studied the art of Kukishinden ryu Happo Hiken jutsu from the Kuki family.

Kukishinden ryu warriors used to wear Yoroi battle armors, therefore strong and direct attacks in certain unarmed points are used. This school also uses Bo Ryaku (special kind of strategy), Sui Ren in Ka Ren (use of water and fire), Onshin Jutsu (disquise) and weapons as Hanbo (90 cm stick), Rokushaku Bo (180 cm stick), Kaginawa (rope with a hook), Kusari Gama (sickle with chain), Bisento (heavy weapon similar to helbard) and Daisharin (axle with two wheels). It is also written, that Kukishinden warriors used masttops for fighting. This system was used as a naval art, and consequently the movements are designed to be used on a ship that is slippery and rocking.