Estrogen fluctuations during the menstrual cycle, puberty, postpartum, or in the menopausal transition are associated with cognitive, affective, and behavioral effects. Additionally, estrogens are essential in hormonal contraception, menopausal hormone therapy, or gender-affirming hormone therapy. This systematic review summarizes findings on the role of estrogens for structure, function, and connectivity of human brain networks. We searched PubMed, Web of Science, and ScienceDirect for neuroimaging articles assessing estrogens published since 2008. We included 54 studies (N = 2,494 participants) on endogenous estrogen, and 28 studies (N = 1,740 participants) on exogenous estrogen conditions. Estrogen-related changes were reported for emotion, reward, memory, and resting-state networks, and in regional white and gray matter, with a particular neural plasticity in the hippocampus and amygdala. By examining study designs, imaging measures, and analysis methods, this review highlights the role of neuroimaging in advancing neuroendocrine and neurocognitive research, particularly promoting brain health for women and individuals with ovaries.