Hunter-gatherers arrived in Japan in Paleolithic times, though little evidence of their presence remains, as Japan's acidic soils are inhospitable to the process of fossilization. However, the discovery of unique edge-ground axes in Japan dated to over 30,000 years ago may be evidence of the first Homo sapiens in Japan. Early humans likely arrived on Japan by sea on watercraft. Evidence of human habitation has been dated to 32,000 years ago in Okinawa's Yamashita Cave and up to 20,000 years ago on Ishigaki Island's Shiraho Saonetabaru Cave.

The Jōmon period is the time in Japanese history, traditionally dated between c. 14,000–300 BCE, during which Japan was inhabited by a diverse hunter-gatherer and early agriculturalist population united through a common Jōmon culture, which reached a considerable degree of sedentism and cultural complexity. The name "cord-marked" was first applied by the American zoologist and orientalist Edward S. Morse, who discovered sherds of pottery in 1877 and subsequently translated it into Japanese as Jōmon. The pottery style characteristic of the first phases of Jōmon culture was decorated by impressing cords into the surface of wet clay and is generally accepted to be among the oldest in the world.

The Jōmon period was rich in tools and jewelry made from bone, stone, shell and antler; pottery figurines and vessels; and lacquerware. It is often compared to pre-Columbian cultures of the North American Pacific Northwest and especially to the Valdivia culture in Ecuador because in these settings cultural complexity developed within a primarily hunting-gathering context with limited use of horticulture.

The Yayoi period is generally accepted to date from 300 BCE to 300 CE. However, although highly controversial, radiocarbon evidence from organic samples attached to pottery shards may suggest a date up to 500 years earlier, between 1,000 BC and 800 BC. During this period Japan transitioned to a settled agricultural society using agricultural methods that were introduced to the country, initially in the Kyushu region, from Korea.

The name Yayoi is borrowed from a location in Tokyo where pottery of the Yayoi period was first found. Yayoi pottery was simply decorated and produced using the same coiling technique previously used in Jōmon pottery. Yayoi craft specialists made bronze ceremonial bells (dōtaku), mirrors, and weapons. By the 1st century AD, Yayoi people began using iron agricultural tools and weapons.

As the Yayoi population increased, the society became more stratified and complex. They wove textiles, lived in permanent farming villages, and constructed buildings with wood and stone. They also accumulated wealth through land ownership and the storage of grain. Such factors promoted the development of distinct social classes. Contemporary Chinese sources described the people as having tattoos and other bodily markings which indicated differences in social status. Yayoi chiefs, in some parts of Kyūshū, appear to have sponsored, and politically manipulated, trade in bronze and other prestige objects. That was made possible by the introduction of an irrigated, wet-rice agriculture from the Yangtze estuary in southern China via the Ryukyu Islands or Korean Peninsula. Wet-rice agriculture led to the development and growth of a sedentary, agrarian society in Japan.

The Kofun period is an era in the history of Japan from about 300 to 538 CE (the date of the introduction of Buddhism), following the Yayoi period. The Kofun and the subsequent Asuka periods are sometimes collectively called the Yamato period. This period is the earliest era of recorded history in Japan, but studies depend heavily on archaeology since the chronology of historical sources tends to be distorted. The word kofun is Japanese for the type of burial mound dating from this era.

It was a period of cultural import. Continuing from the Yayoi period, the Kofun period is characterized by influence from China and the Korean Peninsula; archaeologists consider it a shared culture across the southern Korean Peninsula, Kyūshū and Honshū. On the other hand, the most prosperous keyhole-shaped burial mounds in Japan during this period were approximately 5,000 in Japan from the middle of the 3rd century in the Yayoi period to the 7th century in the Asuka period, and many of them had huge tombs, but in the southern Korean Peninsula there were only 13 from the 5th century to the 6th century, and the tombs were small. Wall decorations and Japanese-style armor, which are characteristic of older Japanese burial mounds, were excavated from 5th century burial mounds in the southern Korean Peninsula. This shows that Japan and the southern Korean Peninsula influenced each other.

According to the Nihon Shoki, Buddhism and the Chinese writing system were introduced near the end of the period from Baekje. The Kofun period recorded Japan's earliest political centralization, when the Yamato clan rose to power in southwestern Japan, established the Imperial House, and helped control trade routes across the region.

The Asuka period was a period in the history of Japan lasting from 538 to 710 (or 592 to 645), although its beginning could be said to overlap with the preceding Kofun period. The Yamato polity evolved greatly during the Asuka period, which is named after the Asuka region, about 25 km south of the modern city of Nara. The Asuka period is characterized by its significant artistic, social, and political transformations, having their origins in the late Kofun period. The introduction of Buddhism marked a change in Japanese society. The Asuka period is also distinguished by the change in the name of the country from Wa to Nippon.

The Nara period of the history of Japan covers the years from 710 to 794 CE. Empress Genmei established the capital of Heijō-kyō (present-day Nara). Except for a five-year period (740–745), when the capital was briefly moved again, it remained the capital of Japanese civilization until Emperor Kanmu established a new capital, Nagaoka-kyō, in 784, before moving to Heian-kyō, modern Kyoto, a decade later in 794. Japanese society during this period was predominately agricultural and centered on village life. Most of the villagers followed Shintoism, a religion based on the worship of natural and ancestral spirits named kami. The capital at Nara was modeled after Chang'an, the capital city of the Tang dynasty. In many other ways, the Japanese upper classes patterned themselves after the Chinese, including adopting the Chinese writing system, Chinese fashion, and a Chinese version of Buddhism.

The Heian period is the last division of classical Japanese history, running from 794 to 1185. It was preceded by the Nara period by the 50th emperor, Emperor Kanmu, when the capital of Japan was moved to Heian-kyō (modern Kyoto) to which the period was named after. It is a period in Japanese history when Chinese influences were in decline and the national culture matured.

The Heian period is also considered the peak of the Japanese imperial court and noted for its art, especially poetry and literature. Two types of Japanese script emerged, including katakana, a phonetic script which was abbreviated into hiragana, a cursive alphabet with a unique writing method distinctive to Japan. This gave rise to Japan's famous vernacular literature, many of which were written by court women who were not as educated in Chinese compared to their male counterparts.

Although the Imperial House of Japan had power on the surface, the real power was in the hands of the Fujiwara clan, a powerful aristocratic family who had intermarried with the imperial family. Many emperors actually had mothers from the Fujiwara family. Heian (平安) means "peace" in Japanese. The entry of the warrior class into court influence was a result of the Hōgen Rebellion. At this time Taira no Kiyomori revived the Fujiwara practices by placing his grandson on the throne to rule Japan by regency. Their clan, the Taira, would not be overthrown until after the Genpei War, which marked the start of the Kamakura shogunate. 

The Kamakura period is a period of Japanese history that marks the governance by the Kamakura shogunate, officially established in 1192 in Kamakura by the first shōgun Minamoto no Yoritomo after the conclusion of the Genpei War, which saw the struggle between the Taira and Minamoto clans. The period is known for the emergence of the samurai, the warrior caste, and for the establishment of feudalism in Japan.

During the early Kamakura period, the shogunate continued warfare against the Northern Fujiwara which was only defeated in 1189. Then, the authority to the Kamakura rulers waned in the 1190s and power was transferred to the powerful Hōjō clan in the early 13th century with the head of the clan as regent (Shikken) under the shogun which became a powerless figurehead. The later Kamakura period saw the invasions of the Mongols in 1274 and again in 1281. To reduce the amount of chaos, the Hōjō rulers decided to decentralize power by allowing two imperial lines – Northern and Southern court, to alternate the throne. In the 1330s, the Southern court under Emperor Go-Daigo revolted and eventually led to the Siege of Kamakura in 1333 which ended the rule of the shogunate. With this, the Kamakura period ended. There was a short re-establishment (1333–1336) of imperial rule under Go-Daigo assisted by Ashikaga Takauji and Nitta Yoshisada but would later lead to direct rule under Ashikaga, forming the Ashikaga shogunate in the succeeding Muromachi period.

Several significant administrative achievements were made during the Hōjō regency. These provided the opportunities for other military lords to exercise judicial and legislative authority and the government established a council centered around collective leadership. The period saw the adoption of Japan's first military code of law in 1232. There was an expansion of Buddhist teachings into Old Buddhism (Kyū Bukkyō) and New Buddhism (Shin Bukkyō).

The Muromachi period (Muromachi jidai, also known as the Muromachi era, the Ashikaga era, or the Ashikaga period) is a division of Japanese history running from approximately 1336 to 1573. The period marks the governance of the Muromachi or Ashikaga shogunate (Muromachi bakufu or Ashikaga bakufu), which was officially established in 1338 by the first Muromachi shōgun, Ashikaga Takauji, two years after the brief Kenmu Restoration (1333–1336) of imperial rule was brought to a close. The period ended in 1573 when the 15th and last shogun of this line, Ashikaga Yoshiaki, was driven out of the capital in Kyoto by Oda Nobunaga. From a cultural perspective, the period can be divided into the Kitayama and Higashiyama periods (later 15th – early 16th centuries). The early years from 1336 to 1392 of the Muromachi period are known as the Nanboku-chō or Northern and Southern Court period. This period is marked by the continued resistance of the supporters of Emperor Go-Daigo, the emperor behind the Kenmu Restoration. The years from 1465 to the end of the Muromachi period are also known as the Sengoku period or Warring States period.

The Azuchi–Momoyama period is the final phase of the Sengoku period in Japanese history from 1568 to 1600. The Azuchi–Momoyama period began with Oda Nobunaga entering into Kyoto in 1568 to install Ashikaga Yoshiaki as the 15th and ultimately final shōgun of the Ashikaga Shogunate, which had collapsed after outbreak of the Ōnin War in 1467 and triggered the chaotic Sengoku period. Nobunaga overthrew Yoshiaki and dissolved the Ashikaga Shogunate in 1573, launching a war of conquest to politically unify Japan by force from his base in Azuchi. Nobunaga was forced to commit suicide in the Honnō-ji Incident in 1582, and his successor Toyotomi Hideyoshi completed his campaign of unification, closing the Sengoku period and enacting reforms to consolidate his rule. Hideyoshi launched the Japanese invasions of Korea in 1592, but the invasion's failure damaged his prestige, and his young son and successor Toyotomi Hideyori was challenged by Tokugawa Ieyasu after his death in 1598. The Azuchi–Momoyama period ended with Tokugawa victory at the Battle of Sekigahara in 1600 – unofficially establishing the Tokugawa Shogunate and beginning the Edo period. The Azuchi–Momoyama period oversaw Japanese society and culture transitioning from the Middle Ages to the early modern period. The Azuchi–Momoyama period is named after Nobunaga's Azuchi Castle and Hideyoshi's Momoyama Castle, and is also known as Shokuhō period in some Japanese texts, abridged from the surnames of the period's two leaders in the on-reading: Shoku (織) for Oda (織田) plus Hō (豊) for Toyotomi (豊臣).

The Edo period or Tokugawa period is between 1603 and 1867 in the history of Japan, when Japan was under the rule of the Tokugawa shogunate and the country's 300 regional daimyō. Emerging from the chaos of the Sengoku period, the Edo period was characterized by economic growth, strict social order, isolationist foreign policies, a stable population, "no more wars", and popular enjoyment of arts and culture. The shogunate was officially established in Edo (now Tokyo) on March 24, 1603, by Tokugawa Ieyasu. The period came to an end with the Meiji Restoration on May 3, 1868, after the fall of Edo.

The Meiji era is an era of Japanese history which extended from October 23, 1868 to July 30, 1912. This era represents the first half of the Empire of Japan, during which period the Japanese people moved from being an isolated feudal society at risk of colonization by Western powers to the new paradigm of a modern, industrialized nation state and emergent great power, influenced by Western scientific, technological, philosophical, political, legal, and aesthetic ideas. As a result of such wholesale adoption of radically different ideas, the changes to Japan were profound, and affected its social structure, internal politics, economy, military, and foreign relations. The period corresponded to the reign of Emperor Meiji. It was preceded by the Keiō era and was succeeded by the Taishō era, upon the accession of Emperor Taishō.

Taishō is a period in the history of Japan dating from 30 July 1912 to 25 December 1926, coinciding with the reign of the Emperor Taishō. The new emperor was a sickly man, which prompted the shift in political power from the old oligarchic group of elder statesmen (or genrō) to the Imperial Diet of Japan and the democratic parties. Thus, the era is considered the time of the liberal movement known as the "Taishō democracy" in Japan; it is usually distinguished from the preceding chaotic Meiji period and the following militaristic-driven first part of the Shōwa period.

The Shōwa era refers to the period of Japanese history corresponding to the reign of Emperor Shōwa (Hirohito) from December 25, 1926 until his death on January 7, 1989. It was preceded by the Taishō period. The pre-1945 and post-war Shōwa periods are almost-completely different states: the pre-1945 Shōwa era (1926–1945) concerns the Empire of Japan, and post-1945 Shōwa era (1945–1989) is the State of Japan. Before 1945, Japan moved into political totalitarianism, ultranationalism and statism culminating in Japan's invasion of China in 1937, part of a global period of social upheavals and conflicts such as the Great Depression and World War II. Defeat in the Second World War brought about radical change in Japan. For the first and only time in its history, Japan was occupied by foreign powers, an American-led occupation which lasted for seven years. Allied occupation brought forth sweeping democratic reforms. It led to the formal end of the emperor's status as a demigod and the transformation of Japan from a form of mixed constitutional and absolute monarchy to a constitutional monarchy with a liberal democracy. In 1952, with the Treaty of San Francisco, Japan became a sovereign nation again. The postwar Shōwa period was characterized by the Japanese economic miracle. The Shōwa era was longer than the reign of any previous Japanese emperor. Emperor Shōwa was both the longest-lived and longest-reigning historical Japanese emperor as well as the longest-reigning monarch in the world at the time. On 7 January 1989, Crown Prince Akihito succeeded to the Chrysanthemum Throne upon the death of his father Emperor Shōwa, which marked the start of the Heisei period.

The Heisei era is the period of Japanese history corresponding to the reign of Emperor Akihito from 8 January 1989 until his abdication on 30 April 2019. The Heisei era started on 8 January 1989, the day after the death of the Emperor Hirohito, when his son, Akihito, acceded to the throne as the 125th Emperor. In accordance with Japanese customs, Hirohito was posthumously renamed "Emperor Shōwa" on 31 January 1989. Heisei translates to "peace everywhere". Thus, 1989 corresponds to Shōwa 64 until 7 January, and Heisei 1 (平成元年, Heisei gannen, gannen means "first Year") from 8 January. The Heisei era ended on 30 April 2019 (Heisei 31), with the abdication of Akihito from the Chrysanthemum Throne. It was succeeded by the Reiwa era as Crown Prince Naruhito ascended the throne on 1 May midnight local time.

Reiwa is the current era of Japan's official calendar. It began on 1 May 2019, the day on which Emperor Akihito's elder son, Naruhito, ascended the throne as the 126th Emperor of Japan. The day before, Emperor Akihito abdicated the Chrysanthemum Throne, marking the end of the Heisei era. Reiwa is interpreted as "beautiful harmony".