Heian period (794–1185)

Originally, the title of Sei-i Taishōgun (Commander-in-Chief of the Expeditionary Force Against the Barbarians) was given to military commanders during the early Heian Period for the duration of military campaigns against the Emishi who resisted the governance of the Imperial court based in Kyoto. Ōtomo no Otomaro became the first Sei-i Taishōgun in history. The most famous of these shoguns was Sakanoue no Tamuramaro who conquered the Emishi in the name of Emperor Kammu. Eventually, the title was abandoned in the later Heian period after the Ainu had been either subjugated or driven to Hokkaidō.

In the later Heian, one more shogun was appointed. Minamoto no Yoshinaka was named sei-i taishōgun during the Gempei War only to be killed shortly thereafter by Minamoto no Yoshitsune.

Kamakura shogunate (1192–1333)

In the early 11th century, daimyo protected by samurai came to dominate internal Japanese politics. Two of the most powerful families, the Taira and Minamoto, fought for control over the declining imperial court. The Taira family seized control from 1160 to 1185, but was defeated by the Minamoto in the Battle of Dan-no-ura. Minamoto no Yoritomo seized certain powers from the central government and aristocracy and established a feudal system based in Kamakura in which the private military, the samurai, gained some political powers while the Emperors of Japan and the aristocracy in Japan remained the de jure rulers. In 1192, Yoritomo was awarded the title of Sei-i Taishōgun by the emperor and the political system he developed with a succession of shogun at the head became known as a shogunate.

Yoritomo's wife's family, the Hōjō, seized the power from the Kamakura shoguns. When Yoritomo's sons and heirs were assassinated, the shogun became a hereditary figurehead. Real power rested with the Hōjō regents. The Kamakura shogunate lasted for almost 150 years, from 1192 to 1333.

In 1274 and 1281, the Mongol Empire launched invasions against Japan. An attempt by Emperor Go-Daigo to restore imperial rule in 1331 was unsuccessful, but weakened the shogunate significantly and led to its eventual downfall.

Kemmu restoration (1333–1336)

The end of the Kamakura shogunate came when Kamakura fell in 1333 and the Hōjō Regency was destroyed. Two imperial families, Go-Saga the senior line, and Go-Daigo the junior line, had a claim to the throne. The problem was solved with the intercession of the Kamakura Shogunate, who had the two lines alternate. This lasted until 1331, when the Go-Daigo line refused to alternate with the Go-Saga line. As a result the Go-Daigo was exiled. Around 1334–1336 Ashikaga Takauji helped the Go-Daigo line regain the throne.

The fight against the shogunate left the new Emperor with too many people claiming a limited supply of land. Ashikaga Takauji turned against the Emperor when the discontent about the distribution of land grew great enough. In 1336 the emperor was banished again, in favor of a new emperor.

During the Kemmu Restoration, after the fall of the Kamakura shogunate in 1333, another short-lived shogun arose. Prince Moriyoshi (also known as Prince Morinaga), son of Emperor Go-Daigo, was awarded the title of Sei-i Taishōgun. However, Prince Moriyoshi was later put under house arrest and, in 1335, killed by Ashikaga Tadayoshi.

Ashikaga shogunate (1336–1573)

In 1338 Ashikaga Takauji, like Yoritomo a descendant of the Minamoto princes, was awarded the title of sei-i taishōgun and established the Ashikaga Shogunate, which lasted until 1573. The Ashikaga had their headquarters in the Muromachi district of Kyoto, and the time period during which they ruled is also known as the Muromachi Period.

Tokugawa shogunate (1603–1868)

Tokugawa Ieyasu seized power and established a government at Edo (now known as Tokyo) in 1600. He received the title sei-i taishōgun in 1603 after he forged a family tree to show he was of Minamoto descent. The Tokugawa shogunate lasted until 1867, when Tokugawa Yoshinobu resigned as shogun and abdicated his authority to Emperor Meiji.

During the Edo period, effective power rested with the Tokugawa shogun, not the emperor in Kyoto, even though the former ostensibly owed his position to the latter. The shogun controlled foreign policy, the military, and feudal patronage. The role of the emperor was ceremonial, similar to the position of the Japanese monarchy after the Second World War.

The title of shogun in Japan meant a military leader equivalent to general, and at various times in the first millennium shoguns held temporary power, but it became a symbol of military control over the county. The establishment of the shogunate (or bakufu) at the end of the twelfth century saw the beginning of samurai control of Japan for 700 years until the Meiji Restoration in the middle of the nineteenth century.

Today the head of the Japanese government is called "prime minister", the usage of the term "shogun" has continued somewhat. A retired prime minister who still wields considerable power and influence behind the scenes is called a yami shogun, or "shadow shogun", a somewhat modern incarnation of the cloistered rule. Examples of shadow shoguns are former prime minister Kakuei Tanaka and the politician Ichirō Ozawa.

The term bakufu originally meant the dwelling and household of a shogun, but in time it came to be generally used for the system of government of a feudal military dictatorship, exercised in the name of the shogun; and this is the meaning that has been adopted into English through the term 'shogunate'.

The shogunate system was originally established under the Kamakura shogunate by Minamoto no Yoritomo. Although theoretically the state, and therefore the Emperor, held ownership of all land of Japan, the system had some feudal elements, with lesser territorial lords pledging their allegiance to greater ones. Samurai were rewarded for their loyalty with agricultural surplus, usually rice, or labor services from peasants. In contrast to European feudal knights, samurai were not land owners. The hierarchy that held this system of government together was reinforced by close ties of loyalty between samurai and their subordinates.

Each shogunate was dynamic, not static. Power was constantly shifting and authority was often ambiguous. The study of the ebbs and flows in this complex history continues to occupy the attention of scholars. Each shogunate encountered competition. Sources of competition included the emperor and the court aristocracy, the remnants of the imperial governmental systems, the shōen system, the great temples and shrines, the shugo and the jitō, the kokujin and early modern daimyo. Each shogunate reflected the necessity of new ways of balancing the changing requirements of central and regional authorities.

• List of shoguns
• History of Japan
• Feudalism
• Daimyo