The city of Higashiomi hosts many historic sites, the most notable being Gamono, which provided the setting for the somonka love poems exchanged between Princess Nukata and Prince Oama in the 7th century.

There are also many ancient temples such as Eigen-ji, Hyakusai-ji, and Ishido-ji. In the middle ages, the area prospered as a key junction for market and temple towns, and in early modern times the city produced many talented entrepreneurs, commonly known as Omi merchants. Through networking between many different areas, Higashiomi developed a unique, multifaceted culture.

Then, in the modern times, came the “Great Consolidation of the Meiji period” on April 1, 1889, and the municipality system was introduced. With the establishment of the Town and Village Consolidation Promotion Law in October 1953, towns and villages in the area were consolidated into one city, five towns, and one village (the Great Consolidation of the Showa period). Aito Village was later incorporated as a town on February 11, 1971.

On February 11, 2005, one city (Yokaichi) and four towns (Eigenji, Gokasho, Aito, and Koto) were consolidated into Higashiomi City, which was subsequently expanded when it merged with the towns of Gamo and Notogawa on January 1, 2006.