Background Heart rate variability (HRV) extracted from electrocardiogram measured for a short period during a resting state is clinically used as a bio-signal reflecting the emotional state. However, as interest in wearable devices increases, greater attention is being paid to HRV extracted from long-term electrocardiogram, which may contain additional clinical information. The purpose of this study was to examine the characteristics of HRV parameters extracted through long-term electrocardiogram and explore the differences between participants with and without depression and anxiety symptoms. Methods Long-term electrocardiogram was acquired from 354 adults with no psychiatric history who underwent Holter monitoring. Evening and nighttime HRV and the ratio of nighttime-to-evening HRV were compared between 127 participants with depressive symptoms and 227 participants without depressive symptoms. Comparisons were also made between participants with and without anxiety symptoms. Results Absolute values of HRV parameters did not differ between groups based on the presence of depressive or anxiety symptoms. Overall, HRV parameters increased at nighttime compared to evening. Participants with depressive symptoms showed a significantly higher nighttime-to-evening ratio of high-frequency HRV than participants without depressive symptoms. The nighttime-to-evening ratio of HRV parameters did not show a significant difference depending on the presence of anxiety symptoms. Conclusion HRV extracted through long-term electrocardiogram showed circadian rhythm. Depression may be associated with changes in the circadian rhythm of parasympathetic tone.