The castle was strategically placed along the Shakujii River, near Sanbō-tera Pond, to control and defend the river valley. Though there may have been another similar fortification erected nearby during the Heian period (794-1185), it is likely that the last incarnation of Shakujii castle was first built after the Kamakura period (1185-1333). A dam was built around the same time, a short distance from the castle, at a spot selected by a diviner, to block the waterway.
The castle lasted into the Muromachi period (1336-1467), and was controlled by the Toshima clan who, supported by Kanrei (Shogun's deputy) Ashikaga Mochiuji, were in their prime during the rebellion of Uesugi Zenshū, which lasted from 1415-1417. However, roughly forty years later, the Toshima took part in the 1477 Kyōtoku Rebellion, supporting the uprising of Nagao Kageharu. Toshima Yasutsune led the forces of Shakujii castle and nearby Nerima castle to reinforce his brother Toshima Yasuaki, who was attacked at Hiratsuka castle. They were defeated by the army of Ōta Dōkan, a vassal of the Uesugi clan, who put down the rebellion. The Toshima then fled to Kotsukue castle, but were defeated there as well, and Shakujii castle was destroyed a short time later.
Recently, attempts have been made to restore the castle. However, there is very little remaining above ground, and even based on what digging has revealed, it has been difficult to determine the exact location, size, and extent of the fortifications and the moat.