The construction of Wat Mahathat was begun during the reign of King Borommarachathirat I in 1374 A.D. but was completed during the reign of King Ramesuan (1388-1395 A.D.). When King Songtham (1610-1628 A.D.) was in power the main prang collapsed. The restoration work on the prang was probably completed in the reign of King Prasatthong (1630-1655 A.D.) Duing the restoration the height of the prang was considerably increased.

Wat Mahathat was reatored once again during the reign of King Borommakot (1732-1758 A.D.) when four porticos of the main prang were added. In 1767 A.D. when Ayutthayawas sacked the wat was burnt and has since then been in ruins.

Wat Mahathat was a royal monastery and has been the seat of the Sangaraja, the head of the Buddhist monks of the kamavasi sect, since the time of the Mahathera Thammakanlavan, who was a contemporary of King Borommarachathirat I, who built the wat. During the reign of King Rama VI in the Rattanakosin period, about 1911 A.D., the main prang of the wat collapsed again and looters seized the opportunity to dig for treasure. Only in 1956 A.D. did the Fine Arts Department undertake excavations around the central area of the prang where the relics must have been kept. The relics of the Buddha were found in the stupa within a seven layer reliquary. Other antiquities were recovered as well, including Buddha images, votive tablete, covered boxes shaped like fish and golden plaques in the form of animals. All these objects are now at the Chao Sam Phraya National Museum.