Manyeonsa Temple is known to have been built in 1208, the fourth year of King Heejong’s (r. 1204-1211) reign during the Goryeo dynasty.

It is said that Manyeonsa Temple was constructed by Great Monk Manyeon after he dreamt of 16 nahans, Buddha’s disciples, preparing to build a temple to preserve Buddha’s statue when taking a short nap during his journey back to Songwangsa Temple in Jogyesan Mountain from Wonhyosa Temple in Mudeungsan Mountain. When he awoke from his nap, he noticed that snow had completely covered his nearby surroundings except for the exact spot where he lied down, which remained so warm that snow had melted and steam was rising from the ground. He then settled in the area by building a dugout where he continued to practice asceticism and later built Manyeonsa Temple.

The temple was partially destroyed during the Korean War (1950) and restoration efforts were made in 1978.