In 1929, astronomers in the faculty of science at Kyoto University built the first astronomical observatory at the summit of Mt. Kwasan, Kyoto-city. However, Kyoto city rapidly grew and developed soon after, and conditions for observing grew worse because of light pollution. Therefore, a plan was initiated in 1961 to find a good site for constructing a new observatory.

After several years (1968), the Hida Observatory was built at Kamitakara-village, Gihu-pref. by transferring the various instruments which had been used at Kwasan Observatory and Mt. Ikoma Solar Observatory. In 1972, a 65 cm refractor telescope (the largest refractor in Asia) was also constructed. Furthermore, in 1979, the Domeless Solar Telescope (DST) was completed, which is the most advanced multiple solar telescope in Japan.

In 2003, the Solar Magnetic Activity Research Telescope (SMART) started its observations. This telescope provides high-resolution H alpha images, and also images of three-dimensional magnetic fields. More recently, the Flare Monitoring Telescope (FMT) was moved from Hida to Ica University in Peru for the purpose of continuous solar observation.