Basal ganglia (BG) are involved in inhibitory control (IC) and known to change in structure and activation along the menstrual cycle. Therefore, we investigated BG activation and connectivity patterns related to IC during different cycle phases. Thirty-six naturally cycling women were scanned three times performing a Stop Signal Task and hormonal levels analysed from saliva samples. We found an impaired Stop signal reaction time (SSRT) during pre-ovulatory compared to menses the higher the baseline IC of women. Blood oxygen level dependent (BOLD)-response in bilateral putamen significantly decreased during the luteal phase. Connectivity strength from the left putamen displayed an interactive effect of cycle and IC. During pre-ovulatory the connectivity with anterior cingulate cortex and left inferior parietal lobe was significantly stronger the higher the IC, and during luteal with left supplementary motor area. Right putamen's activation and left hemisphere's connectivity predicted the SSRT across participants. Therefore, we propose a compensatory mechanism for the hormonal changes across the menstrual cycle based on a lateralized pattern.