He became heir apparent in 1268, and in 1274 received the throne from his father, Emperor Kameyama, to become the ninety-first sovereign. In 1287 he abdicated in favor of his cousin, who became Emperor Fushimi. Ordinarily the throne passed to a direct descendant, but because Emperor Gosaga had died in 1272 without leaving any clear instructions as to who his successor should be, a struggle broke out between Emperor Gofukakusa and Emperor Kameyama, each trying to insure that his own heirs should succeed to the throne.
The contention lasted for over one hundred years (leading eventually to the so-called period of the Northern and Southern Courts [(1336-92]], when the descendants of Emperor Gofukakusa claimed the throne in Kyoto, while the descendants of Emperor Kameyama made the same claim from their retreat in Yoshino to the south). In an attempt to put a stop to the quarrel, Emperor Gouda, who in spite of his abdication some years earlier had retained considerable power, arranged for the throne to pass to his son, Emperor Godaigo, in 1321, but this did not heal the strife.