The effects of the isoflavone daidzein on the ciliary beat distance (CBD, which is a parameter assessing the amplitude of ciliary beating) and the ciliary beat frequency (CBF) were examined in ciliated human nasal epithelial cells (cHNECs) in primary culture. Daidzein decreased [Cl−]i and enhanced CBD in cHNECs. The CBD increase that was stimulated by daidzein was mimicked by Cl−-free NO3− solution and bumetanide (an inhibitor of Na+/K+/2Cl− cotransport), both of which decreased [Cl−]i. Moreover, the CBD increase was inhibited by 5-Nitro-2-(3-phenylpropylamino)benzoic acid (NPPB, a Cl− channel blocker), which increased [Cl−]i. CBF was also decreased by NPPB. The rate of [Cl−]i decrease evoked by Cl−-free NO3− solution was enhanced by daidzein. These results suggest that daidzein activates Cl− channels in cHNECs. Moreover, daidzein enhanced the microbead transport driven by beating cilia in the cell sheet of cHNECs, suggesting that an increase in CBD enhances ciliary transport. An [Cl−]i decrease enhanced CBD, but not CBF, in cHNECs at 37 °C, although it enhanced both at 25 °C. Intracellular Cl− affects both CBD and CBF in a temperature-dependent manner. In conclusion, daidzein, which activates Cl− channels to decrease [Cl−]i, stimulated CBD increase in cHNECs at 37 °C. CBD is a crucial factor that can increase ciliary transport in the airways under physiological conditions.