Toyotomi Hideyoshi had earlier established a similar practice of requiring his feudal lords to keep their wives and heirs at Osaka Castle or the nearby vicinity as hostages to ensure their loyalty. Following the Battle of Sekigahara and the establishment of the Tokugawa Shogunate, this practice was continued at the new capital of Edo as a matter of custom. It was made compulsory for the tozama daimyōs in 1635, and for the fudai daimyōs from 1642. Aside from an eight-year period under the rule of Tokugawa Yoshimune, the law remained in force until 1862.

The sankin-kōtai system forced daimyōs to reside in Edo in alternating sequence, spending a certain amount of time in Edo, and a certain amount of time in their home provinces. It is often said that one of the key goals of this policy was to prevent the daimyōs from amassing too much wealth or power by separating them from their home provinces, and by forcing them to regularly devote a sizable sum to funding the immense travel expenses associated with the journey (along with a large entourage) to and from Edo. The system also involved the daimyōs' wives and heirs remaining in Edo, disconnected from their lord and from their home province, serving essentially as hostages who might be harmed or killed if the daimyōs were to plot rebellion against the shogunate.

With hundreds of daimyōs entering or leaving Edo each year, processions were almost daily occurrences in the shogunal capital. The main routes to the provinces were the kaidō. Special lodgings, the honjin, were available to daimyōs during their travels. The frequent travel of the daimyo encouraged road building and the construction of inns and facilities along the routes, generating economic activity.

King Louis XIV of France instituted a similar practice upon the completion of his palace at Versailles, requiring the French nobility, particularly the ancient Noblesse d'épée ("nobility of the sword") to spend six months of each year at the palace, for reasons similar to those of the Japanese shōguns. The nobles were expected to assist the king in his daily duties and state and personal functions, including meals, parties, and, for the privileged, rising from and getting into bed, bathing, and going to church.