Traditional time and frequency-based heart rate variability (HRV) analysis assumes linearity and may fail to capture the complex, nonlinear dynamics and adaptive capacity of cardiac control. Tone and entropy are nonlinear measures of HRV and may offer a more comprehensive assessment of the autonomic nervous system (ANS) activity. However, current methods are predominantly time-based. Here, we propose a novel frequency-based method to estimate tone and entropy within the same frequency bands commonly used in HRV analysis which are the very low frequency (VLF), LF, and high frequency (HF). Electrocardiogram (ECG) data were collected from 6 healthy male participants (31 ± 4) years old during rest and following intravenous administration of propranolol (0.2 mg/kg) and atropine (0.04 mg/kg). Tone and entropy were computed using both the time-based conventional method and the proposed frequency-based approach for comparison. Frequency-based entropy significantly decreased after atropine across all frequency bands (p < 0.05), with no significant changes under propranolol. Tone differed sig- nificantly between control and propranolol in LF and VLF bands (p < 0.05), but not after atropine. The effect of propranolol on tone was not apparent in the conventional tone assessment, suggesting that our method may provide a complementary evaluation of entropy and tone.