INTRODUCTION: There is controversy about the repercussions of high speed-low amplitude thrust (HVLAT) manipulation in the thoracic region on the autonomic nervous system. OBJECTIVE: To evaluate the immediate effects of the HVLAT in the high thoracic region on the heart rate autonomic modulation of judo athletes. METHODS: In the experimental study, thirty-eight healthy men divided into 2 groups (Judo athletes and non-athletes) having heart rate variability (HRV) collected beat-to-beat using a cardio-pacemater during all stages of the manipulation: i) rest, ii) time 1 (participant positioning), iii) time 2 (positioning of the participant together with the therapist), iv) HVLAT manipulation, v) post 5min, vi) post 10min and vii) post 15min HVLAT. Systolic blood pressure (SBP), diastolic blood pressure (DBP), breath frequency (BF), and HRV were also analyzed. RESULTS: A higher sympathetic modulation was observed with an increase in the standard deviation of successive normal R-R intervals (SDNN) and SD2 indices representing the total variability, however, there was no significant statistical difference in the root mean square of the mean squared differences (RMSSD), percentual of interval differences of successive NN intervals greater than 50 ms (pNN50), and SD1 variables, which represent the parasympathetic nervous system. CONCLUSION: HVLAT manipulation was able to decrease HRV during manipulation, reflecting sympathetic hyperactivity. However, the return of the HRV indices to the baseline conditions in the first minutes of recovery in Judo athletes and non-athletes reflected the safety of the application of the manipulation in these conditions studied.