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Background Menstrual-related migraine (MRM) is a subtype of migraine that significantly impacts women. Despite its high prevalence, MRM remains under-researched compared to other migraine types. This study investigates the phenotypic characteristics and treatment outcomes of MRM compared to non-menstrual migraine (non-MRM). Methods This cross-sectional study included women aged 18 years or older with a diagnosis of migraine and an established menstruation pattern. Informed consent was properly obtained from all participants from the Stanford Headache Clinic and surrounding community between 2014 and 2024 prior to participation in the study. Data were collected from self-reported surveys, including demographic information, headache characteristics, physical and mental health status, and treatment outcomes from the Stanford Headache Clinic and surrounding community. Participants were then categorized into MRM and non-MRM groups. An exploratory analysis was performed to investigate phenotypic features, treatment outcomes, and brain volume through magnetic resonance imaging (MRI) study for each group. Statistical analyses included descriptive statistics, analysis of covariance (ANCOVA), and logistic regression. Results A total of 84 subjects were included, with 38 in the MRM group and 46 in the non-MRM group. The mean age of participants was 34 (SD = 9) years. The MRM group (mean age 38 ± 9) showed significantly higher prevalences of recent change in migraine frequency, migraine attacks occurring in the same site, prodromal signs, speech aura, nausea, and vomiting associated with migraine, and a higher prevalence of reported family history of headache as compared with the non-MRM group (mean age 31 ± 10) (p < 0.05). MRM group also showed significantly higher rate of migraine improvement following the use of triptans and the overall acute and preventive medications (p < 0.05). No significant differences were found in brain volumes between the groups (p > 0.05). Conclusion The MRM group was associated with significantly more bothersome symptoms associated with migraine, higher family history of headache, and more favorable response to overall acute medication especially triptan as compared with the non-MRM group.