In 749 her father turned over the throne to her, making her the forty-sixth ruler of Japan, though her mother, in conjunction with Fujiwara no Nakamaro, continued to exercise actual power.
In 757 Tenno Koken removed Prince Funado from the position of heir apparent and replaced him with Prince Oi, who enjoyed the backing of Fujiwara no Nakamaro. The move aroused considerable opposition at court and even led to plans for a coup d’etat, but these were discovered before any decisive move could be made. Empress Koken then relinquished the throne to Prince Oi, who became Emperor Junnin. Fujiwara no Nakamaro originally enjoyed the trust of Empress Koken and was able to exercise great power in affairs of state, but later he was replaced in the empress’s favor by the Buddhist monk Dokyo. In 764 he attempted to overthrow Dokyo, but his efforts ended in failure. As a result, Emperor Junnin was obliged to abdicate, turning over the throne to the empress, who ascended it a second time, this time becoming known as Empress Shotoku. Tenno Koken in turn prepared to turn over the throne to Dokyo, but was opposed in this move by the ministers of the court.
Koken's reign was turbulent, and she survived coup attempts by both Tachibana no Naramaro and Fujiwara no Nakamaro.
Today, she is remembered chiefly for her alleged affair with a Buddhist monk named Dokyo, a man she honored with titles and power. An oracle from Usa Shrine, the shrine of the kami Hachiman in Usa, is said to have proclaimed that the monk should be made emperor, but when the empress sent Wake no Kiyomaro to verify the pronouncement, Hachiman decreed that only one of imperial blood should ascend to the throne.
Tenno Koken was also known for sponsoring the Hyakumanto Darani, one of the largest productions of printed works in early Japan.
When Tenno Koken died in 770, Dokyo was exiled to the province of Shimotsuke.