Rhyolite is a common volcanic rock; however, few studies have focused on the remanent magnetization of rhyolite lava, and few paleomagnetic studies have successfully investigated rhyolite lavas. We suspect that problems associated with paleomagnetic studies of rhyolite may be due to the nearly ubiquitous flow structure in rhyolite lava. In this study, we examined a thick rhyolite lava flow with clearly marked flow structure to assess its ability to record a consistent paleomagnetic direction, using material penetrated by two drill cores. Progressive thermal demagnetization isolated two magnetization components. A high-temperature component from each of the two cores yields inclinations that differ from each other. The low-temperature component had those that agreed with each other, and were also consistent with the direction expected from a geocentric axial dipole field. The modification of direction of the high-temperature component may be explained by post-magnetization acquisition tilting. The development of flow structure also leads to distortion of directions of the component, which is observed at stratigraphic positions where the volume fraction of light-colored parts of the flow structure >30%. In the case of silicic lava, the low-temperature component may retain directions parallel to the ambient field direction at the time of lava emplacement.