Hormonal fluctuations across the menstrual cycle exert broad influences on brain function and emotional regulation, and evidence linking these changes to anxiety remains inconsistent. This variability may reflect the frequent treatment of anxiety as a single construct, despite substantial evidence that it comprises multiple dimensions. The present study identified a specific relationship in how menstrual cycling status moderates the impact of several internalizing dimensions, including anxiety, depression, and negative affect, on amygdala–hippocampus functional connectivity during a 2-back working memory task. Using data from the Human Connectome Project (N = 389), participants were categorized into three groups based on self-reported menstrual status: follicular phase, luteal phase, or oral contraceptive users. Functional connectivity between the right amygdala and right hippocampus was estimated from fMRI data using the Yale Brain Atlas. Hierarchical regression analyses revealed an interaction between anxious arousal and cycling status. This effect persisted with other predictors already in the model, indicating specificity for that type of anxiety. Among naturally cycling participants, higher anxious arousal was associated with stronger amygdala–hippocampus connectivity. The relationship was reversed in oral contraceptive users, for whom higher anxious arousal predicted lower connectivity. These findings suggest that endogenous hormonal cycling modulates the neural coupling of limbic regions implicated in emotion and memory, with particular sensitivity to somatic anxiety. Understanding how menstrual cycle status shapes anxiety-related neural dynamics can clarify inconsistencies in the literature and advance precision approaches to studying internalizing disorders in women.