The original castle was built here in 1603 by Kato Yoshiakira. It had a large 5 storey tenshu that was actually moved to Aizu when Kato was transferred there in 1627. Tadachika Gamoh became the new lord of Matsuyama castle and completed construction of the Ninomaru before he died in 1635, leaving no heirs.

In 1635, Matsudaira Sadayuki moved into Matsuyama Castle and the Matsudaira family ruled over the area the end of feudalism. Sadayuki rebuilt the donjon with three stories in 1642. This donjon was struck by lightning and burned down on New Year's day in 1784. The construction of the current donjon was not begun until 1820 and not completed until 1854. From 1926 on, many of the yagura, gates and other structures were destroyed by arson and bombings in WWII.

As a relative of the Tokugawa shogun, Matsudaira Sadaaki naturally fought for the Tokugawa in several battles at the Meiji Restoration. Once the emperor regained political power, Sadaaki was a wanted man and considered an enemy of the emperor. In order to avoid attack, he decided to submit and allow Tosa soldiers into the castle while he sought penance and refuge in Joshinji temple in Matsuyama. His sincerity was accepted and thus Sadaaki and Matsuyama Castle were saved from attack.

The Matsudaira family eventually gave the castle to the city of Matsuyama in 1923. The city has been working since 1966 to repair the original structures and rebuild those that were destroyed.