The Phu Khao Thong chedi is situated about two kilometres northwest of the city island. It was built by King Ramesuan in 1387. Burengnong, the Burmese king, built three layers of the large superimposed base in the Burmese style after he seized Ayutthaya in 1569 and named it Phu Khao Thong. The main body of the Thai-style chedi was built later.

King Borom Kot carried out renovations during his reign in 1744 and changed its appearance into a 12- cornered chedi. Only the lowest part retains its original Mon style. According to the records, a canal was dug from Wat Phu Khao Thong by a former monk of the temple to keep the Burmese army out when Ayutthaya was under Burmese attack in 1548. The moat which connects a canal with the main river is still in evidence and is called Mahanak canal in honor of the former monk.

However, after Ayutthaya fell to the Burmese in 1767 the whole place was burned down. The Thai Government, under Premier Pibulsongkram, renovated the shrine again approximately 40 years ago.