Archeological research indicates that Japan had already been occupied by early humans at least 500,000 years ago, during the Lower Paleolithic period. Over repeated ice-ages during the last million years, Japan was regularly connected by land bridges to the Asian mainland (by Sakhalin to the North, and probably Kyushu to the South), facilitating migrations of humans, animals and plants to the Japanese archipelago from the area that is now China and Korea.

With the end of the last ice-age and general warming, the Jomon culture emerged around 11,000 BC, characterized by a mesolithic to neolithic semi-sedentary hunter-gatherer lifestyle and the manufacture of the earliest known pottery in the World. It is thought that Jomon populations were the ancestors of the Proto-Japanese and today's Ainu.

The start of the Yayoi period around 300 BC marked the influx from the Asian mainland of new technologies such as rice-farming, as well as rather massive migrations from various part of Asia like Korea and China, especially around Beijing and Shanghai, and from the South by marine route. However, several recent studies have pointed out that Yayoi period is 500 to 600 longer than previously believed making massive immigrations uneeded to explain the increase in population.

According to traditional Japanese mythology, Japan was founded in the 7th century BC by the ancestral Emperor Jimmu. During the 5th and 6th centuries, the Chinese writing system and Buddhism were introduced with other Chinese cultures first via the Korean peninsula and later directly from China. The emperors were the nominal rulers, but actual power was usually held by powerful court nobles, regents, or shoguns (military governors).

Ancient political structure held that, once battles between rivals were finished, the victorious Shogun would migrate to the capital Heian (fully Heian-kyo-to, 'kyo-to' meaning capital city, and the full name now shortened to the suffix, 'Kyoto') to rule under the grace of the Emperor. However, in the year 1185, general Minamoto no Yoritomo was the first to break this tradition, refusing to relocate and subsequently holding power in Kamakura, just south of present-day Yokohama. While this Kamakura Shogunate was somewhat stable, Japan soon fell into warring factions and suffered through what became known as the Warring States or Sengoku Period. In the year 1600, at the Battle of Sekigahara, Shogun Tokugawa Ieyasu either co-opted or defeated his enemies and formed the Tokugawa Shogunate in the small fishing village of Edo (formerly transcribed as 'Yeddo'), what is now known as Tokyo (eastern capital).

During the 16th century, traders from Portugal, the Netherlands, England, and Spain arrived, as did Christian missionaries. During the early part of the 17th century, Japan's shogunate suspected that they were actually forerunners of a military conquest by European powers and ultimately barred all relations with the outside world except for severely restricted contacts with Dutch and Chinese merchants at Nagasaki (Dejima) with occasional Korean envoys. This isolation lasted for 251 years, until Commodore Matthew Perry forced the opening of Japan to the West with the Convention of Kanagawa in 1854.

Within several years, renewed contact with the West profoundly altered Japanese society. Following the 1867-1868 Boshin War the shogunate was forced to resign, and the emperor was restored to power. The Meiji Restoration of 1868 initiated many reforms. The feudal system was abolished and numerous Western institutions were adopted, including a Western legal system and government, along with other economic, social and military reforms that transformed the Empire of Japan into a world power. As results of Sino-Japanese war and Russo-Japanese war, Japan acquired Taiwan, Sakhalin, and the Kuril Islands, and later annexed Korea in 1910.

The early 20th century saw Japan come under increasing influence of an expansionist military, leading to the invasion of Manchuria, a second Sino-Japanese War (1937). Japan allied with Germany and Italy and formed the Axis Pact. Japanese leaders felt it was necessary to attack the US naval base in Pearl Harbor (1941) to ensure Japanese supremacy in the Pacific. However, the entry of the United States into World War II would slowly tilt the balance in the Pacific against the Japanese. After a long Pacific campaign, Japan lost Okinawa in the Ryukyu islands and was pushed back to the four main islands. The United States made fierce attacks on Tokyo, Osaka, and other cities by strategic bombing, and Hiroshima and Nagasaki with two atomic bombs. Japan eventually agreed to an unconditional surrender to the United States on August 15, 1945.

A defeated post-war Japan remained under US occupation until 1952, whereafter it embarked on a remarkable economic recovery that returned prosperity to the islands. The success of 1964 Tokyo Olympic Games is regarded as many as the sign that Japan had finally regained its national status. The Ryukyu islands remained under US occupation until 1972 to stabilize East Asia, and a major military presence remains there to this day. The Soviet Union seized the Kuril islands north of Hokkaido at the end of WWII, and despite the collapse of the Soviet state and friendly relations between countries, Russia has refused to return these islands.