[2] The Shoku Nihongi records that in 741, as the country recovered from a major smallpox epidemic, Emperor Shōmu ordered that a monastery and nunnery be established in every province, the kokubunji (国分寺).

[3][4] These temples were built to a semi-standardized template, and served both to spread Buddhist orthodoxy to the provinces, and to emphasize the power of the Nara period centralized government under the Ritsuryō system.

Per changes in the style of roof tiles, only 14 of the 64 kokubunji temples known retained much of their original structure to the end of the Kamakura period, and it appears that the Bungo Kokubun-ji was one of them.

In 1240, the Ōtomo clan, who had been appointed shugo of the province by the Kamakura shogunate, brought in the famous monk Ninshō from Saidai-ji in Nara to revitalize the temple.

Additionally, the Oita City Historical Museum has been constructed on adjacent land, displaying a restored model of Bungo Kokubunji's seven-storied pagoda and artifacts excavated.