Previous neuroimaging research has demonstrated that female gonadal hormones can alter the structure and function of adult women's brains. So far, we do not know how hormonal contraceptives affect female brain structure, in part because within-person longitudinal observations are lacking. Here, we compared 28 young women before and after three months of regular contraceptive intake with 28 naturally cycling women of comparable age. The goal was to explore within-person neural change in women using contraceptives. Neuroimaging, hormonal, cognitive, and affect data were collected at two time points for each participant. A voxel-wise whole-brain comparison of both groups revealed decreased gray matter volume in the left amygdala/anterior parahippocampal gyrus in women using contraceptives as compared to the control group. Resting-state functional connectivity of this region with the dorsolateral prefrontal cortex changed from positive to negative connectivity following contraceptive intake whereas the opposite held for the control group. An exploratory analysis revealed that gray matter volume in the left amygdala/anterior parahippocampal gyrus was associated with positive affect at the second time point. There were no systematic differences in cognitive performance change between the groups. These findings provide initial insights into effects of hormonal contraceptives on the human brain and expand previous findings on hormone-related amygdala/hippocampal complex plasticity. The affected brain regions may be related to psychological wellbeing, underlining the importance of future studies on contraceptive-induced brain changes.