Sphingomyelin synthase (SMS) catalyzes the conversion of phosphatidylcholine and ceramide to sphingomyelin and diacylglycerol. We previously showed that SMS1 deficiency leads to a reduction in expression of the K+ channel KCNQ1 in the inner ear, causing hearing loss. However, it remains unknown whether this change in expression is attributable to a cellular process or a systemic effect in the knockout animal. Here, we examined whether manipulation of SMS1 activity affects KCNQ1/KCNE1 currents in individual cells. To this end, we expressed the KCNQ1/KCNE1 channel in human embryonic kidney 293T cells, and evaluated the effect of SMS1 manipulations on the channel using whole-cell recording. Application of tricyclodecan-9-yl-xanthogenate, a non-specific inhibitor of SMSs, significantly reduced current density and altered channel voltage dependence. Knockdown of SMS1 by an shRNA, however, reduced current density alone. Consistent with this, overexpression of SMS1 increased the current density without changing channel properties. Furthermore, application of a protein kinase D (PKD) inhibitors also suppressed current density without changing channel properties; this effect was non-additive with that of SMS1 shRNA. These results suggest that SMS1 positively regulates KCNQ1/KCNE1 channel density in a PKD-dependent manner.