Japan's medieval era was characterized by the emergence of a ruling class of warriors, the samurai. In the year 1185, general Minamoto no Yoritomo was the first to break the tradition of ruling alongside the emperor in Kyoto, holding power in distant Kamakura. After Yoritomo's death, another warrior clan, the Hojo, came to rule as regents for the shoguns. The shogunate managed to repel Mongol invasions from Mongol-occupied Korea in 1274 and 1281. The Kamakura shogunate lasted another fifty years. Its successor, the Muromachi shogunate was much weaker, and Japan soon fell into warring factions. The "Warring States" or Sengoku period ensued.

A group of Portuguese Foreigners in Japan in the 17th century

During the 16th century, traders and missionaries from Portugal reached Japan for the first time, initiating the Nanban ("southern barbarian") period of active commercial and cultural exchange between Japan and the West (and even China). During the last quarter of this century, Oda Nobunaga, Toyotomi Hideyoshi, and Tokugawa Ieyasu established increasingly strong control over the warring states of Japan. Toyotomi reunified the country, and following his death, Tokugawa seized power by defeating his enemies at the Battle of Sekigahara in 1600, moving the capital to Edo (now Tokyo) and starting the Tokugawa shogunate.

The Tokugawa shogunate, suspicious of the influence of Catholic missionaries, barred all relations with Europeans, except for severely restricted contacts with Dutch merchants at the artificial island of Dejima. They also became more conscious of trade with China, especially after the Manchu conquered China and established the Qing Dynasty. The Manchus subjugated Korea in 1637, and the Japanese feared an invasion. Thus, the country became more isolated than ever before. This period of isolation lasted for two and a half centuries, a time of tenuous political unity known as the Edo period, considered to be the height of Japan's medieval culture.