The term "naginata" first appeared in the Kojiki in 712 CE and was used by Sohei warrior priests during the Nara Period, around 750 CE. In the paintings of battlefield scenes made during the Tengyo no Ran in 936 CE, the naginata can be seen in use. It was in 1086, in the book Oshu Gosannenki (A Diary of Three Years in Oshu,) that the use of the naginata in combat is first recorded. In this period the naginata was regarded as an extremely effective weapon by warriors.

During the Gempei War (1180-1185), in which the Taira clan was pitted against Minamoto no Yoritomo of the Minamoto clan, the naginata rose to a position of particularly high esteem. Cavalry battles had become more important by this time, and the naginata proved excellent at dismounting cavalry and disabling riders. The widespread adoption of the naginata as a battlefield weapon forced the introduction of sune-ate (shin guards) as a part of Japanese armor. The rise of importance for the Naginata can be seen as being mirrored by the European pike, another long pole weapon used to defeat mounted warriors. An excellent example of the role of women in Japanese society and martial culture at this time is Itagaki, who, famous for her naginata skills, led the garrison of 3,000 warriors stationed at Toeizakayama castle. Ten thousand Hojo clan warriors were dispatched to take the castle, and Itagaki led her troops out of the castle, killing a significant number of the attackers before being overpowered.

During the Edo Period, as the naginata became less useful for men on the battlefield, it became a symbol of the social status of women of the samurai class. A functional naginata was often a traditional part of a samurai daughter's dowry. Although they did not typically fight as normal soldiers, women of the samurai class were expected to be capable of defending their homes while their husbands were away at war. The naginata was considered one of the weapons most suitable for women, as it allows a woman to keep a male opponent at a distance, where his greater height, weight, and upper body strength offers less of an advantage.

By the 17th century the rise in popularity of firearms caused a great decrease in the appearance of the naginata on the battlefield.

Due to the influence of westernization after the Meiji Restoration the perceived value of martial arts, naginata included, dropped severely. It was from this time that the focus of training became the strengthening of the will and the forging of the mind and body. During the Showa period, naginata training became a part of the public school system.

Martial arts training in Japan was banned for five years by the Allied Forces after Japan's surrender at the end of World War II. After the lifting of the ban in 1950, a modern form of naginata training, known as Atarashii Naginata (New Naginata), was developed. Since World War II naginata has primarily been practiced as a sport, rather than as military training, with a particular emphasis on etiquette and discipline.

The naginata also has been a favorite among the shaolin.