Arai Checkpoint was established in 1600 and was originally called Inagire Sekisho (checkpoint) throughout the Edo Period. This is because the checkpoint was originally located near Imagire-guchi—the point where Lake Hamana meets the Pacific Ocean. However, due to two natural disasters in 1699 and 1707, the checkpoint was moved to its present location.
Under orders of the Tokugawa Shogunate, checkpoints were set up to monitor travelers at strategic portions of the old Tōkaidō Road that linked the Shogun’s capital of Edo (Tokyo) with the Imperial capital of Kyoto. These checkpoints were important means of control for the Shogunate as they restricted the flow of guns and other contraband into Edo and made sure that the wives or daughters of feudal lords were not sneaking out of Edo without passes, The wives and children of daimyo were virtual hostages in Edo to help ensure the good behavior of the daimyo when the were back in their home fiefs.
The Shogunate directly controlled the Arai Checkpoint until 1702, when the job of overseeing its activities was handed over to the daimyo who ruled the fief of Yoshida, in Mikawa (present day Toyohashi in Aichi Prefecture). The current structure dates back to 1855, when it was rebuilt over a three-year period following the massive damage it received at the hands of a major earthquake in 1854. This is the only originally surviving checkpoint left in Japan. In 1955, the Japanese government designated the Arai Checkpoint a special historical site.