Circadian rhythms are endogenous oscillations of approximately 24-h periods and regulate diel changes in physiological biochemical processes. We examined the effects of black ginger (Kaempferia parviflora) on the expression of circadian clock genes and the disruption of circadian rhythms using in vitro and in vivo assays. K. parviflora extract increased the amplitude of circadian rhythms, extended the circadian period, and caused phase delays in NIH3T3 cells. We identified chemical components involved in the circadian clock gene expression using high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance. 3,5,7,3′,4′-Pentamethoxyflavone, 5,7,4′-trimethoxyflavone, and 5,7-dimethoxyflavone were identified as components that regulated the circadian clock gene expression. In addition, we examined the effects of K. parviflora on behavioral entrainment in mice subjected to experimental jet lag (6-h phase advance), finding that K. parviflora enhanced adaptation to jet lag. These results suggested that polymethoxyflavones in K. parviflora could regulate the circadian clock and reduce circadian disruption.