In the fourth year of her reign (645), Naka no Oe no Oji killed SOGA no Emishi and his son Iruka (Isshi no hen [the Murder in the Year of Isshi], Taika no Kaishin [Great Reformation of the Taika Era]) and Empress Kogyoku handed the Imperial throne over to Prince Karu, her younger maternal half-brother (later, Emperor Kotoku) (this was the first abdication of the throne in history).
在位4年目（645年）に中大兄皇子が蘇我蝦夷・入鹿親子を滅ぼす（乙巳の変・大化の改新）と、皇極天皇は同母弟の軽皇子（後の孝徳天皇）に皇位を譲った（史上初の譲位）。