BACKGROUND: Individuals with arterial hypertension often have an autonomic nervous system (ANS) imbalance with predominance of sympathetic ANS. This predominance can lead to injury of several organs affecting its functioning. There is evidence that performing high intensity resistance training (RT) with heavier loads and a lower number of repetitions results in lower cardiovascular stress when compared with lighter loads and a higher number of repetitions. However, the effects of different protocols of RT in autonomic modulation are not known. Therefore, the aim of the study was to analyze and compare the effects of different protocols of high intensity of effort RT on autonomic cardiac modulation of hypertensive women. METHODS: A randomized crossover design clinical trial was conducted with 15 postmenopausal hypertensive women who underwent a control session and two high intensity RT protocols involving 6 and 15 repetition maximum (RM). Heart rate variability (HRV), systolic blood pressure (SBP), diastolic blood pressure (DBP), heart rate (HR) and double product (DP) were collected pre, immediately post, 1 h post, and 24 h post each protocol. Repeated-measures ANOVA were used. RESULTS: SBP was higher for 6RM than control immediately after session (p < 0.05). There were no differences for DBP among protocols (p ≥ 0.05). HR was higher for 15RM than 6RM and control immediately after and 1 h after session (p ≤ 0.05). DP values for 15RM were significantly higher than 6RM and control immediately after the session and remained higher than control 1 h after session (p ≤ 0.05). The indices that compose HRV (rMSSD) were lower after 15RM than 6RM and control (p ≥ 0.05). The parameters of parasympathetic activity (HF) were decreased and sympathetic (LF) activity was increased for 15RM when compared to the 6RM and control session immediately after the exercise session (p ≤ 0.05). CONCLUSION: Performing high intensity RT with lower loads and a higher number of repetitions seems to promote acute increases in sympathetic ANS activity, which may be related to cardiovascular stress. On the other hand, heavier load and lower repetition RT did not significantly impact upon autonomic modulation when compared to a control session.