Heart rate variability (HRV), systolic blood pressure variability (BPV), and spontaneous baroreflex sensitivity (BRS) are indirect and approximate measures of autonomic regulation of the cardiovascular system. Studies have shown differences in HRV and BRS between males and females; however, no study has observed differences in BPV, HRV, or BRS between male and female athletes. One hundred males (age 21.2 ± 2.1 y; BMI 27.4 ± 4.5 kg/m2) and sixty-five females (age: 19.7 ± 1.6 y; BMI 22.7 ± 2.2 kg/m2) were assessed during the pre-season baseline. We collected resting beat-to-beat blood pressure and R-R intervals using finger photoplethysmography and a 3-lead electrocardiogram, respectively. Participants underwent a controlled slow breathing protocol (six breaths/minute: 5 s inhale, 5 s exhale) for 5 min. Spectral and linear analysis was conducted on blood pressure and ECG data. Regression curves were fitted to the blood pressure and R-R signals, with the slopes providing the BRS parameters. Male athletes had significantly (p < 0.05) lower mean heart rate, RR interval SD2/SD1, HRV % low-frequency, and higher BP high-frequency power during controlled respiration. No differences were found in any BRS parameters. HRV and BPV responses to a slow breathing protocol differed between male and female athletes; however, BRS responses did not.