Background/Objective: The quarantine caused by the COVID-19 pandemic increased sedentary behavior, psychological stress, and sleep disturbances in the population favoring the installation of alterations in the cardiovascular system. In this sense, physical exercise has widely been suggested as an efficient treatment to improve health. The current study determined the impact of short-term high-intensity circuit training (HICT) on resting heart rate variability (HRV) in adults. Methods: Nine healthy participants (age: 31.9 ± 4.4 yr.) performed 36 HICT sessions (3 times per day; 3 days per week) and four participants (age: 29.5 ± 1.7 yr.) were assigned to a control group. The HICT consisted of 12 min of whole-body exercises performed during a workout. Twenty-four hours before and after the exercise program, HRV parameters were recorded. Results: The heart rate exercise during the last session trended to be lower when compared with the first HICT session (p = 0.07, d = 0.39, 95% CI = −13.50, 0.72). The interval training did not modify the HRV time (Mean NN, SDNN, RMSSD, NN50, pNN50) and frequency (LF, HF, LF/HF ratio, total power) domain parameters. Conclusion: Thirty-six HICT sessions did not provide enough stimuli to modify the resting HRV in adults during social isolation elicited by the COVID-19 pandemic. However, the data suggested that exercise protocol did not induce cardio-vagal adaptations.