It is said that the temple was founded by order of Emperor Tenmu in 673 and that it subsequently maintained numerous magnificent rows of halls and buildings as a Buddhist temple attached to the nearby Hine Jinja Shrine (Oiseki Daimyojin) until they burnt down in the attack of Kishu by Toyotomi Hideyoshi in 1585. Although Toyotomi Hideyori restored the temple, the two-storied pagoda and main hall are the only buildings that have survived since the temple’s early days. At the time of its foundation, it was named “Izekiyama Ganjojuji Jufukuin” and was also called “Oizeki Gobo” (Oizeki Temple).

While Muhenko-in Temple, which is depicted in the center of the Painting of Hineno Village, was the temple where Kujo Masamoto first resided and was used as the headquarters for the shoen, it is theorized that Jigen-in Temple (former Nakanobo of Oizeki Jinja Shrine) was the successor to Muhenko-in Temple.

The current name, which came from the Buddhist name of Kujo Masamoto, “Jigen-in,” was given by the head priest of Ninnaji Temple in Kyoto in the Edo period (1603-1868) to make Jigen-in Temple a branch of Ninnaji Temple of the Omuro school of the Shingon sect of Buddhism.

The two-story pagoda was erected in 1271 and is the only National Treasure in Izumisano City. It is one of the three famous two-story pagodas in Japan, together with the pagoda of Ishiyamadera Temple in Shiga and that of Kongosanmai-in Temple on Mt. Koya in Wakayama. It is 10.5 meters high, and its lower story is square in shape, with each side being 2.7 meters long. The roof is supported by nitesaki (bracket complex composed of two steps) and decorated with nokishirin (convex struts). The upper story features 12 columns arranged in a circle, and a two-stage structure of odaruki (tail rafters) and nokishirin is formed with yontesaki (four-step bracket complexes) to further enhance the roof, which is covered with cypress bark shingles. A seated figure of Dainichi Nyorai (a Tangible Cultural Property designated by Osaka Prefecture) is enshrined on the shumidan (alter) in the inner sanctuary along with the attendants Jikokuten (Dhrtarastra) and Tamonten (Vaisravana). They used to be kept next to the main hall but were relocated to their current location when the shrine was restored during the Meiji period (1868-1912).