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Background: Limited studies have measured the burden of migraine in Japan. This study aimed at estimating the disease burden of migraine in Japan and identifying factors associated with the burden using the 2017 National Health and Wellness Survey., Methods: Migraine patients were defined by ICHD-3 like criteria with ≥4 monthly headache days (MHDs), and non-migraine respondents were selected using 1:4 propensity score matching. Multivariate analyses were conducted to compare Health-related Quality of Life (HRQoL), work productivity and activity impairment (WPAI), healthcare resource utilization (HRU) and costs between the two groups, and to identify factors associated with these outcomes in migraine patients., Results: In 30,001 respondents, 378 migraine patients were identified. Compared to matched controls (N = 1512), migraine patients had lower physical (45.17 vs. 49.89), mental (42.28 vs. 47.71) and role/social (37.91 vs. 44.19) component summary scores (p < 0.001). Migraine patients had higher absenteeism (6.4% vs. 2.2%), presenteeism (40.2% vs. 22.5%), total work productivity impairment (44.3% vs. 24.5%), total activity impairment (45.0% vs. 23.9%), indirect costs (1,492,520 JPY vs. 808,320 JPY) and more visits to healthcare providers in the past 6 months (7.23 vs. 3.96) (p < 0.001). More MHDs was associated with worse HRQoL, and higher HRU and indirect costs., Conclusions: Japanese migraine patients experience an incremental burden. This demonstrates the unmet needs among Japanese migraine patients.