The 2016 Kumamoto earthquake occurred in the tectonically complex central Kyushu area where several forcing factors such as the subducting Philippine Sea plate, the Median Tectonic Line and the Nankai forearc sliver, the spreading Okinawa trough, and the migrating volcanic front are involved. Neogene–Quaternary tectonics of central Kyushu are revisited by integrating geological, seismological, and geodetical approaches. Deformation histories of the Futagawa and Hinagu fault zones, the source faults of the Kumamoto earthquake, are also established in an attempt to explain the relationship between geologic structures and rupture processes of the earthquake. The results show that present-day tectonics surrounding central Kyushu are considered to have originated in the last 1 Ma or younger, as a transtensional tectonic zone (Central Kyushu Shear Zone) characterized by combined dextral faults and rift zones (or volcanoes). Reflecting spatiotemporal variations of the crustal stress field and rift activity, the Futagawa and Hinagu fault zones show multi-stage deformation throughout the Neogene–Quaternary periods: normal faulting to dextral faulting for the Futagawa fault zone and sinistral to dextral faulting for the Hinagu fault zone. Those diverse histories of stress and strain fields in central Kyushu possibly led to the complexities of fault geometry and rupture process of the Kumamoto earthquake.