In 1333, Emperor Go-Daigo initiated a revolt to reclaim authority for the imperial court. He initially had the support of General Ashikaga Takauji, but their alliance fell apart when Go-Daigo refused to appoint Takauji shōgun. Takauji turned against the Emperor in 1338, seizing Kyoto and installing a rival, Emperor Kōmyō, who appointed him shogun.^[45] Go-Daigo escaped to Yoshino, setting up a rival Southern Court and starting a long conflict with the Northern Court established by Takauji in Kyoto.^[46] The Shogunate faced ongoing challenges from regional lords, called daimyōs, who grew increasingly autonomous.

Ashikaga Yoshimitsu, Takauji's grandson, took power in 1368 and was the most successful in consolidating shogunate power. He ended the civil war between the Northern and Southern Courts in 1392. However, by 1467, Japan entered another tumultuous period with the Ōnin War, which originated from a succession dispute. The country fragmented into hundreds of independent states ruled by daimyōs, effectively diminishing the shogun's power.^[47] Daimyōs battled each other to seize control over different parts of Japan.^[48] Two of the most formidable daimyōs of this time were Uesugi Kenshin and Takeda Shingen.^[49] Not just the daimyōs, but also insurrectionist peasants and "warrior monks" linked to Buddhist temples took up arms, forming their own military forces.^[50]

During this Warring States period, the first Europeans, Portuguese traders, arrived in Japan in 1543,^[51] introducing firearms and Christianity.^[52] By 1556, daimyōs were using about 300,000 muskets,^[53] and Christianity gained a significant following. Portuguese trade was initially welcomed, and cities like Nagasaki became bustling trade hubs under the protection of daimyōs who had converted to Christianity. The warlord Oda Nobunaga capitalized on European technology to gain power, initiating the Azuchi–Momoyama period in 1573.

Despite the internal conflicts, Japan experienced economic prosperity that started during the Kamakura period. By 1450, Japan's population reached ten million,^[41] and commerce flourished, including significant trade with China and Korea.^[54] The era also saw the development of iconic Japanese art forms like ink wash painting, ikebana, bonsai, Noh theather, and the tea ceremony.^[55] Although plagued by ineffective leadership, the period was culturally rich, with landmarks like Kyoto's Kinkaku-ji, the "Temple of the Golden Pavilion," being built in 1397.^[56]