Shiga was known as Ōmi Province or Gōshū before the prefectural system was established. Omi was a neighbor of Nara and Kyoto, at the junction of western and eastern Japan. During the period 667 to 672, Emperor Tenji founded a palace in Otsu. In 742, Emperor Shōmu founded a palace in Shigaraki. In the early Heian Period, Saichō was born in the north of Otsu and founded Enryaku-ji, the center of Tendai and one a UNESCO World Heritage Site and monument of Ancient Kyoto now.
In the Medieval Period, the Sasaki clan ruled Omi, and afterward the Rokkaku clan, Kyōgoku clan and Azai clans ruled Omi. In the 1570s, Oda Nobunaga subjugated Omi and built Azuchi Castle on the eastern shores of Lake Biwa in 1579. Tōdō Takatora, Gamō Ujisato, Oichi, Yodo-dono, Ohatsu and Oeyo were Omi notables in the Sengoku Period. In those times, Ninja were active in Kōka (See also Kōga-ryū).
In 1600, Ishida Mitsunari, born in the east of Nagahama and based in Sawayama Castle, made war against Tokugawa Ieyasu in Sekigahara, Gifu. After the battle, Ieyasu made Ii Naomasa a new lord of Sawayama. Naomasa established the Hikone Domain, later famous for Ii Naosuke. Ii Naosuke became the Tokugawa shogunate's Tairō and concluded commercial treaties with the Western powers and thus ended Japan's isolation from the world in the 19th century. Besides the Hikone Domain, many domains ruled Omi such as Zeze.
With the abolition of the han system, eight prefectures were formed in Omi. They were unified into Shiga Prefecture in September 1872. "Shiga Prefecture" was named after "Shiga District" because Otsu belonged to the district until 1898. From August 1876 to February 1881, southern Fukui Prefecture had been incorporated into Shiga Prefecture.