Hypertension is one of the most prevalent diseases and a risk factor for stroke and cardiovascular disease. Our previous study indicated a negative correlation between fat intake and blood pressure in subjects with a fat mass and obesity-associated gene variant. We investigated the effects of four fatty acid groups on blood pressure in healthy Japanese women with the gene variants, including the involvement of body mass index. A total of 227 Japanese women aged 18-64 years completed a 3-day nutritional intake diary and their blood pressure was measured. The single nucleotide polymorphism rs9939609 of the gene was genotyped, and the participants were divided into two genetic groups (those with or without at least one minor allele). Spearman's rank correlation coefficient was applied to investigate the relationships between the fatty acids and blood pressure. A path analysis was performed to determine the effect of fatty acids on blood pressure including the involvement of body mass index. In the group with the gene variant, a significant negative correlation was detected between saturated fatty acid intake and systolic and diastolic blood pressures, and between monounsaturated fatty acid intake and only diastolic blood pressure. In a path analysis of both systolic and diastolic blood pressures, the path from only saturated fatty acid intake to blood pressure was significant, but the path from saturated fatty acids to body mass index was not significant. These results suggest that saturated fatty acid intake, without the involvement of body mass index, may be associated with the lower systolic and diastolic blood pressures in healthy Japanese women with a fat mass and obesity-associated gene variant.