Anarchism in Japan began to emerge in the late 19th and early 20th centuries, as Western anarchist literature began to be translated into Japanese. It existed throughout the 20th century in various forms, despite repression by the state that became particularly harsh during the two world wars, and it reached its height in the 1920s with organisations such as Kokuren and Zenkoku Jiren.

Japanese anarchism had a number of notable leading figures who dominated the movement at different times. The first of these leaders was Kōtoku Shūsui, who led the development of an anarchist faction within existing left-wing movements, which then split into its own independent movement in the first decade of the 1900s. Kōtoku was executed for treason in 1911, and the movement was subject to severe repression for a decade. The next leading figure was Ōsugi Sakae, who involved himself heavily in support for anarcho-syndicalism and helped to bring the movement out of its 'winter period', until he was murdered by military police in 1923.

Another leading figure was Hatta Shūzō, who reoriented the anarchist movement in a more anarcho-communist direction during the late 1920s, opposing labour unions as a tool of revolution. This produced a split between anarcho-syndicalists and anarcho-communists, which dominated anarchist politics and weakened the movement. From 1931 onwards, the anarchist movement was suppressed more harshly due to the wartime policies of the Empire of Japan. After the war, an anarchist movement once again appeared (the Japanese Anarchist Federation) and was led by important pre-war anarchists such as Iwasa Sakutarō and Ishikawa Sanshirō, but it was once again weakened by splits between the two factions.

From very early on in the history of Japanese anarchism, the movement was in close contact with anarchists from Europe, America, and elsewhere in Asia. Japanese anarcho-syndicalist ideas were often inspired by French syndicalists, and works by writers such as Peter Kropotkin and Emma Goldman had a great influence on the Japanese anarchist movement.

Andō Shōeki, an eighteenth-century Japanese doctor and philosopher, is sometimes considered to be proto-anarchist in thought. He advocated what was described by Bowen Raddeker as "what we might call mutual aid", and he challenged the hierarchical relationships in Japanese society, including the hierarchy between the sexes. In 1908, the early socialist and anarchist Japanese newspaper Nihon Heimin Shinbun described him as an anarchist.

The communalist structure of some agricultural villages during the Tokugawa era is also seen as being proto-anarchist. One individual who would become an anarchist in his adult life, Iwasa Sakutarō, was born in a farming hamlet in the early Meiji era. His grandfather had used his influence as headman to encourage communal farming practices, resulting in the creation of a "half-communist village". This helped to inspire Iwasa to believe in the possibility of an anarchist society.

Modern anarchist ideas first had an influence in Japan on the extreme end of the Japanese liberal movement. In the 1880s, the rise of the pro-democracy Freedom and People's Rights Movement coincided with the prominent assassination of Alexander II of Russia by left-wing extremists, and historian Tsuzuki claimed that "the ideal figure for Liberal extremists was said to be an assassin." Kōtoku Shūsui, who would later become a leading anarchist, started off as a supporter of liberal parties including the Rikken Jiyūtō in the 1890s, even acting as the English translator for their newspaper for two years. When the liberal faction joined the new right-wing Rikken Seiyūkai party in 1900, however, Kōtoku became disillusioned with liberalism. He was attracted to socialism instead, and quickly involved himself in the budding socialist movement.

In 1898, Kōtoku joined the staff of the Yorozu Chūhō newspaper, wherein he published an article in 1900 condemning war in Manchuria. He published his first book in 1901, titled Imperialism, Monster of the Twentieth Century, which was a monumental work in the history of Japanese leftism, criticising both Japanese and Western imperialism from the point of view of a revolutionary socialist. In May 1901, Kōtoku was involved in the founding of the first Social Democratic Party in Japan. It was immediately outlawed under the 1900 Peace Preservation Law, despite its commitment to parliamentary tactics. In 1903, he also wrote the book Quintessence of Socialism, acknowledging influence from Karl Marx.