Nardilysin (NRDC) is a metalloprotease of the M16 family, which has multiple functions such as enhancing the ectodomain shedding of membrane proteins in the extracellular space and regulating transcription in the nucleus. NRDC-deficient mice (Nrdc-/-) show various phenotypes such as hypomyelination, hypothermia, and bradycardia. In the present study, we have focused on the role of NRDC in regulating heart rate and obtained the following results: (1) The intrinsic heart rate, determined by pharmacological blocking of the autonomic nervous system, was significantly reduced in Nrdc-/-; (2) Funny (If) current and T-type calcium current were significantly reduced in isolated Nrdc-/- sinus node cells; (3) Messenger RNA levels of Cav3.1 and HCN1/4, ion channels involved in sinus automaticity, were markedly decreased in Nrdc-/- hearts; (4) Gene knockdown of NRDC in primary rat cardiomyocytes reduced HCN1/4 mRNA levels; (5) Chromatin immunoprecipitation PCR showed NRDC binding to the promoter regions of Cav3.1 and HCN1/4; (6) Reintroduction of wild-type NRDC, but not the enzymatically inactive mutant of NRDC (E>A mutant), into NRDC-deficient cells restored HCN1 mRNA expression; (7) NRDC-E>A mutant knock in mice showed bradycardia and significantly reduced intrinsic heart rate, suggesting that NRDC enzyme activity is important for the control of heart rate. Together, our results indicate that NRDC in cardiomyocyte controls heart rate through the transcriptional regulation of ion channels critical for sinus automaticity.