The history of pottery making in Toki area appears to have started more than 1300 years ago, with of Mino ware dating to the 16th century during the Azuchi-Momoyama period.

In the post-Meiji restoration cadastral reforms, Toki District in Gifu Prefecture was created, and the village of Tokiguchi was established on July 1, 1889 by the creation of the modern municipalities system.

The city of Toki was incorporated on February 1, 1955, with the area formerly divided among 5 towns (Tokitsu, Oroshi, Tsumagi, Dachi, and Izumi) and 3 villages (Tsurusato, Sogi and Hida).

In January 2004, a referendum held to decide whether Toki should merge with its neighboring municipalities, the cities and town of Tajimi, Mizunami and Kasahara, failed to obtain majority support.

The city is home to the Large Helical Device, a stellarator investigating plasma physics with an eye towards fusion power generation.