Before it became a Confucian academy, Byeongsanseowon Confucian Academy was originally located in Pungsang-hyeon under the name Pungakseodang School, which was used as a educational institution since the Goryeo dynasty by a political party known as the Sarim Party. It was moved to its current location in Byeongsan by a well-respected Confucian scholar named Yu Seong-nyong, penname Seoae, in 1572.

When Yu Seong-nyong passed away in 1607, many of his followers and other renowned scholars commemorated the late Confucian scholar by building Jondeoksa Shrine to enshrine his ancestral tablet in 1613, followed by renaming of the institution to Byeongsanseowon in 1614. Yu Seong-nyong's ancestral tablet was later moved to Yeogangseowon to be placed together with the ancestral tablet of Toegye Yi Hwang. In 1629, another ancestral tablet of the late scholar was made and housed in Jondeoksa Shrine.

In 1863, Byeongsanseowon was recognized by the king to receive support as a private Confucian academy. The lecture hall and shrine were reconstructed in 1921 and 1937 respectively as part of preservation efforts made during the Japanese occupation. This academy is designated as Historic Site No. 260, housing a collection of 1,000 documents and 3,000 books, including works by Yu Seong-nyong.