He succeeded to the throne in 1072, taking the reign name Shirakawa, after his father, the emperor Go-Sanjō, had abdicated in his favour. His ascendancy came at a time when the encroachment of private landed estates (shōen) on the public domain seriously threatened the economic foundations of the imperial government. The warrior monks of the nearby temples threatened the capital city of Kyōto, and the weakening of the Fujiwara family, which had dominated the emperors for two centuries, made for bitter factionalism within the court, a situation that gave the emperor the chance to reassert his authority.
Shirakawa abdicated in 1086 and as retired emperor (jōkō) succeeded in retaining power in opposition to the Fujiwara regent. He established an administrative centre replete with judicial functions and military guard. This was the cloister government through which all the subsequent emperors until 1185 exercised power after abdicating. Shirakawa, however, had scant interest in reform. Although at first he sought to reduce private estates, he soon gave up the effort and became instrumental in converting large tracts of public domain into imperial shōen. With these sources of wealth he lavishly patronized Buddhism. He failed, however, to strengthen the imperial government, and he was unable to prevent the rise of the provincial warrior gentry.