On January 11, 1198, Emperor Tsuchimikado took over the Imperial Throne, but Emperor Go-Toba continued to run his cloister government as a retired emperor for 23 years until 1221, spanning three generations starting from Emperor Tsuchimikado and continuing to Emperor Juntoku and Emperor Chukyo.
建久9年（1198年）1月11日、土御門天皇に譲位し、以後、土御門、順徳天皇、仲恭天皇と承久三年（1221年）まで、3代23年間に渡り太上天皇として院政を敷く。