The brain operates in a flexible dynamic regime, generating complex patterns of activity (i.e neuronal avalanches). This study aimed to describe how brain dynamics change according to menstrual cycle (MC) phases. Brain activation patterns were estimated from resting state magnetoencephalography (MEG) scans, acquired women at early follicular (T1), peri-ovulatory (T2) and mid-luteal (T3) phases of MC. We investigated the functional repertoire (number of ways in which large bursts of activity spread through the brain) and the region-specific influence on large-scale dynamics across MC. Finally, we assessed the relationship between sex hormones and changes in brain dynamics. A significantly larger number of visited configuration patterns, in T2 than in T1, in the beta frequency band was observed. No relationship between changes in brain dynamics and sex hormones was showed. Finally, we showed that, in the beta band, the left posterior cingulate gyrus and the right insula were more present in the functional repertoire in T2 than in T1, while the right pallidum was more present in T1 than in T2. In summary, we showed a hormone independent increase of brain dynamics during the ovulatory phase. Moreover, we demonstrated that several specific brain regions play a key role in determining this change.