Intake of omega-3 polyunsaturated fatty acids (PUFAs) has favorable effects on the prevention of postpartum depression, but fish, the principal source of omega-3 PUFAs, are becoming a depleted resource. We therefore examined whether lower periconceptional intake of omega-6 PUFAs, whose metabolic pathways are antagonistic to those of omega-3 PUFAs, is associated with lower prevalence of postpartum depression while simultaneously considering omega-3 PUFA intake. The participants were 92,595 mothers involved in the ongoing Japan Environment and Children's Study. Periconceptional intakes of omega-6 and -3 PUFA were measured using a food frequency questionnaire. Postpartum depression was assessed using the Edinburgh Postnatal Depression Scale. Generalized additive mixed model analysis was used to draw contour plots of postpartum depression on a plane with omega-6 and omega-3 PUFA intakes on the x- and y-axes, respectively. The adjusted prevalence ranged from 11.0% to 26.3% within the respective 1st to 99th percentile intake ranges and monotonously decreased with decreasing omega-6 PUFA intake. In contrast, the prevalence decreased with increasing omega-3 PUFA intake, but the trend almost disappeared above 2 g/day. Our results highlight the potential importance of focusing on omega-6 PUFAs as well as omega-3 PUFAs prior to conception to reduce postpartum depression.