Assessing cardiac dynamics over time is essential for understanding cardiovascular health and its parallel patterns of activity with the brain. We present a methodology to estimate the time-resolved sympathetic and parasympathetic modulations of cardiac dynamics, specifically tailored for the rat heart. To evaluate the performance of our method, we study a dataset comprising spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats. These rats were administered dobutamine to elicit autonomic dynamics. The results obtained from our method demonstrated accurate time-resolved depiction of sympathetic reactivity induced by dobutamine administration. These responses closely resembled the expected autonomic alterations observed during physical exercise conditions, albeit emulated pharmacologically. We further compared our method with standard measures of low-frequency (LF) and high-frequency (HF) components, which are commonly used, although debated, for sympathetic and parasympathetic activity estimation. The comparisons with LF and HF measures further confirmed the effectiveness of our method in better capturing autonomic changes in rat cardiac dynamics. Our findings highlight the potential of our adapted method for time-resolved analysis in future clinical and translational studies involving rodent models. The validation of our approach in animal models opens new avenues for investigating the relationship between ongoing changes in cardiac activity and parallel changes in brain dynamics. Such investigations are crucial for advancing our understanding of the brain-heart connection, particularly in cases involving neurodegeneration, brain injuries and cardiovascular conditions. KEY POINTS: We developed a method for time-resolved estimation of sympathetic and parasympathetic modulations in rat cardiac dynamics, validated against standard low-frequency and high-frequency measures. We used a cohort of spontaneously hypertensive rats and Wistar-Kyoto rats, with dobutamine administration to induce autonomic responses. Our method accurately depicted time-resolved sympathetic reactivity similar to autonomic changes during physical exercise. Our findings suggest potential for future clinical and translational studies on the brain-heart connection, particularly in cardiovascular conditions.