Baroreceptors respond to fluctuations in blood pressure (BP) by modifying physiology in order to maintain a homeostatic set point. Baroreflex sensitivity (BRS) is used to quantify baroreceptor function and is a useful metric for tracking cardiovascular disease state and treatment effects. Pathological conditions such as hypertension (HTN) alter baroreflex function and reduce BRS. Traditionally, the sequence method is used to measure BRS, in which the linear slope of concomitant changes in BP and RR intervals are assessed. However, in rats, a high respiratory rate reduces the reliability of the sequence method. Here, we present a modified sequence method that captures BRS at lower frequencies and decreases the variability of the BRS estimate. This method was demonstrated using ECG and BP data from two groups of HTN rats: Sham rats and rats treated with vagus nerve stimulation. The modified sequence method resulted in lower BRS estimates than the traditional sequence technique when applied to the same data sets. Additionally, the modified sequence method resulted in lower BRS estimate variability.