This study examined the cardiac autonomic responses, as measured by heart rate variability (HRV), during cycling exercise and short-term rest after energy drink consumption. Seventeen participants (seven males and 10 females; age: 22.8 ± 3.5 years; BMI: 24.3 ± 3.3 kg/m2) completed this double-blind, placebo-controlled, counterbalanced crossover design study. Participants received an energy drink formula containing 140 mg of caffeine and a placebo in a randomized order before completing a 10-min steady-state warm up (WUP) and a graded exercise test to exhaustion (GXT) followed by a 15-min short-term rest (STR) period. Heartbeat intervals were recorded using a heart rate monitor. Data were divided into WUP, GXT, and STR phases, and HRV parameters were averaged within each phase. Additionally, root mean square of the standard deviation of R–R intervals (RMSSD) during GXT was analyzed to determine the HRV threshold. Separate two-way (sex (male vs. female) x drink (energy drink vs. placebo)) repeated measures ANOVA were utilized. Significant increases in high frequency (HF) and RMSSD were shown during WUP after energy drink consumption, while interactions between drink and sex were observed for HRV threshold parameters (initial RMSSD and rate of RMSSD decline). No significant differences were noted during STR. Energy drink consumption may influence cardiac autonomic responses during low-intensity exercise, and sex-based differences in response to graded exercise to exhaustion may exist.