After becoming increasingly disillusioned with the Kamakura shogunate over time, Takauji joined the banished Emperor Go-Daigo and Kusunoki Masashige, and seized Kyoto.

Go-Daigo was enthroned once more as emperor, reestablishing the primacy of the Imperial court in Kyoto and starting the so-called Kenmu Restoration.

[5]: 15–21 However, shortly thereafter, the samurai clans became increasingly disillusioned with the reestablished imperial court, which sought to return to the social and political systems of the Heian period.

Taking up the cause of his fellow samurai, he claimed the title of Sei-i Taishōgun and allotted land to his followers without permission from the court.

After defeating the Kikuchi clan at Hakata Bay in the Battle of Tatarahama (1336), Takauji was "virtually master of Kyushu".

[5]: 48–50 At the decisive Battle of Minatogawa in 1336, Takauji defeated Yoshisada again and killed Masashige, allowing him to seize Kyoto for good.

Because of the anomalous situation, which he had himself created and which saw two Emperors reign simultaneously, one in Yoshino and one in Kyoto, the years in which Takauji was shōgun as reckoned by the Gregorian calendar are identified in Japanese historical records by two different series of Japanese era names (nengō), that following the datation used by the legitimate Southern Court and that formulated by the pretender Northern Court.