BACKGROUND: Higher income population tend to prefer brand-name to generic drugs, which may cause disparity in access to brand-name drugs among income groups. A potential policy that can resolve such disparity is imposing a greater co-payment rate on high-income enrollees. However, the effects of such policy are unknown. We examined how patients' choice between brand-name and generic drugs are affected by the unique income-based co-payment rates in Japan; 10% for general enrollees and 30% for those with high income among the elderly aged 75 and over. METHODS: We drew on cross-sectional price variation among commonly prescribed 311 drugs using health insurance claims data from a large prefecture in Japan between October 2013 and September 2014 to identify between-income-group differences in responses to differentiated payments. RESULTS: Running 311 multivariate logistic regression models controlling individual demographics, the median estimate indicated that high-income group was 3% (odds ratio = 0.97) less likely to choose a generic drug than the general-income group and the interquartile estimates ranged 0.92-1.02. The multivariate feasible generalized least squares model indicated high-income group's higher likelihood to choose brand-name drugs than the general-income group without co-payment rate differentiation (p < 0.001). Such gap in the likelihood was attenuated by 0.4% (p = 0.027) with an US$1 increase in the difference in additional payment/month for brand-name drugs between income groups - no gap with US$10 additional payment/month. This attenuation was observed in drugs for chronic diseases only, not for acute diseases. CONCLUSIONS: Income-based co-payment rates appeared to reduce disparity in access to brand-name drugs across income groups, in addition to reducing total medical expenditure among high-income group who shifted from brand-name drugs to generic ones due to larger drug price differences.