Wat Na Khuean is an ancient temple that was established during the reign of King Rama V.  It was officially granted permission for construction in 1862 (B.E. 2405). Later, in 1957 (B.E. 2500), the temple was left abandoned for a period, with no resident monks.

In 1960 (B.E. 2503), Phra Khru Srisatyaphiwat appointed Phra Prakob Sitadhammo as the acting abbot, becoming the first abbot of Wat Na Khuean.

The temple was granted  Visungkhamsima—the consecrated boundary for monastic ceremonies—around 1909 (B.E. 2452), with dimensions of 6.50 meters in width and 11.50 meters in length. The first major restoration was carried out around 1934 (B.E. 2477), and the second around 1969 (B.E. 2512).

Wat Na Khuean received its official temple status certificate from the Chonburi Provincial Office of Buddhism in accordance with Section 31 of the Sangha Act B.E. 2505, as amended by the Sangha Act (No. 2) B.E. 2535, on February 9, 2010.