Katō Kiyomasa, a contemporary of Toyotomi Hideyoshi, was made daimyō of half of the (old) administrative region of Higo in 1588. After that, Kiyomasa built Kumamoto Castle. Due to its many innovative defensive designs, Kumamoto Castle was considered impregnable, and Kiyomasa enjoyed a reputation as one of the finest castle-builders in Japanese history. After Kiyomasa died in 1611, his son, Tadahiro, succeeded him. Tadahiro was removed by Tokugawa Iemitsu in 1632, replacing him with the Hosokawa clan. The current administrative body of the City of Kumamoto was founded on April 1, 1889.
Near the end of World War II, Kumamoto experienced several air raids. The largest one was on the night of June 30 to July 1, 1945. About one third of the city was burned, and more than 300 people died. After the effects of the air raids, the Japanese Buddhist monk Nichidatsu Fujii decided to construct a Peace Pagoda atop Mount Hanaoka in the city to commemorate all those lost in war and to promote peace. Inaugurated in 1954, this pagoda held significance: It inspired Fujii and his followers to build over 80 more around the world including India, Sri Lanka, the United States and the United Kingdom.
On February 1, 1991, the towns of Akita, Kawachi, Tenmei and Hokubu (all from Hōtaku District) were merged into Kumamoto. On October 6, 2008, the town of Tomiai (from Shimomashiki District) was merged into Kumamoto. On March 23, 2010, the town of Jōnan (also from Shimomashiki District) and the town of Ueki (from Kamoto District) were merged into Kumamoto.
A series of earthquakes struck the area beginning April 14, 2016, including a tremor with moment magnitude 7.1 early in the morning of April 16, 2016, local time.