Heart rate exhibits diurnal variation with slower rhythms during sleep. While neural factors were assumed responsible, this study tested whether intrinsic pacemaking contributes. The day-night difference in the average heart rate of mice was independent of fluctuations in average locomotor activity and persisted under pharmacological, surgical, and transgenic interruption of autonomic input to the heart. Spontaneous beating rate of isolated (denervated) sinus node preparations exhibited a day-night rhythm concomitant with rhythmic messenger RNA expression of ion channels including HCN4. In vitro studies demonstrated 24-hour rhythms in the human HCN4 promoter and the corresponding funny current. The day-night heart rate difference in mice was abolished by HCN block, both in vivo and in the isolated sinus node. Circadian clock factors including BMAL1 and Cryptochrome showed rhythmic expression in the sinus node. Disrupting the local clock abolished the day-night HCN4 variation and intrinsic rate differences. Chromatin immunoprecipitation revealed specific BMAL1 binding sites on Hcn4, linking the local clock with intrinsic rate control. The circadian variation in heart rate involves sinus node local clock-dependent Hcn4 rhythmicity. These data reveal a novel regulator of heart rate and mechanistic insight into bradycardia during sleep.