To examine associations between work-family conflict and self-rated health among Japanese workers and to determine whether the associations differed by household income. Data was derived from the Japan Public Health Center-based Prospective Study for the Next Generation in Saku area in 2011-2012 (7,663 men and 7,070 women). Multivariate odds ratios (ORs) and 95% confidence intervals (CIs) for poor self-rated health by work-family conflict consisting of two dimensions (work-to-family and family-to-work conflicts) were calculated by gender and household income. Multivariate ORs of high work-to-family and family-to-work conflicts for poor self-rated health were 2.46 (95% CI; 2.04-2.97) for men and 3.54 (95% CI; 2.92-4.30) for women, with reference to the low work-to-family and family-to-work conflicts (p-value for gender interaction = 0.02). Subgroup analysis indicated that health effects of work-family conflict were likely to be more evident in the low income group only among women. Work-family conflict was associated with poor self-rated health among middle-aged Japanese men and women; its health impact was relatively stronger among women, and particularly economically disadvantaged women.