Stress fields and rotation of the basement of the Beppu Bay Formation are estimated numerically, and the relationships between them and the fault distribution observed in and around Beppu Bay are discussed. The stress field of the Beppu Bay Formation, representing a pull-apart basin formed by right-lateral motion of the Median Tectonic Line and the Kurume-Hiji Line in the Quaternary, is estimated by reproducing the fault motions on the relevant tectonic lines. The estimated stresses are then reexamined in terms of the tensile strength and Coulomb failure criterion to derive a tectonic interpretation of the fault distribution in and around Beppu Bay. It is shown that the Asamigawa Fault and the Tsuzura-Shonai Fault are secondary faults associated with the motions on the Median Tectonic Line, whereas the Beppu Bay cross fault is a secondary fault formed as a result of movement on the Kurume-Hiji Line. The rotation of the basement, formed by the right-lateral motion of the Median Tectonic Line and the Kurume-Hiji Line, is estimated and compared to the distribution of faults and folding in the sedimentary strata of Beppu Bay. It is shown, based on this comparison, that the rotational motion of the basement, or the right-lateral motion of the Median Tectonic Line and Kurume-Hiji Line as a source of rotational motion, appear to control the formation of tectonic structures in Beppu Bay. However, listric faulting and anticlinal folding around the eastern termination of the Kurume-Hiji Line cannot be explained in terms of the rotation of the basement alone, suggesting the involvement of another unrevealed process of faulting and folding in this area.