Wat Bowonniwet was built in the reign of King Rama III, by Somdet Phra Woraratchao Maha Sakdipollasep. In 1923, during the reign of King Rama VI, the nearby Wat Rangsi Sutthawat and Wat Bowon were combined into one temple.
In 1836, during his monkhood, the future King Mongkut (Rama IV) arrived at the temple and became its first abbot. Rama VI and Rama VII also resided at the temple as monks for a time, as did King Bhumibol Adulyadej.