AKI is an established risk factor for developing CKD. Recently, the renoprotective effect of omega-3 polyunsaturated fatty acids (ω3PUFAs) has attracted attention. This study aimed to evaluate the effect of ω3PUFAs on the transition of AKI to CKD, and to identify fatty acid active metabolites in renal tissue. Two mice models of AKI to CKD (7-week, male) and unilateral ureteral obstruction (UUO)-induced renal fibrosis (11-week, male) were fed linseed oil, rich in ω3PUFAs (Lin group), or with soybean oil, low in ω3PUFAs (Soy group). Renal fatty acids and metabolites composition in mice were measured by liquid chromatography-mass spectrometry. Rat renal fibroblast cells (NRK-49F cells) were used for in vitro study. At day 14 after 35 min bilateral renal ischemia reperfusion (IR), significant increase in survival was observed in the Lin group compared to the Soy group. Using the 30 min bilateral renal IR model (AKI to CKD model), the Lin group showed attenuated renal tissue damage and fibrosis. In addition, the antifibrotic effect of Lin group was also observed in UUO renal fibrosis model. In the two mice models, levels of eicosapentaenoic acid (EPA) and its metabolites were significantly elevated in renal tissue of mice fed with Lin. Cultured NRK-49F incubated with EPA and its metabolites 18-hydroxyeicosapentaenoic acid (18-HEPE), 17,18-epoxyeicosatetraenoic acid (17,18-EpETE) and 17,18-dihydroxyeicosatetraenoic acid (17,18-diHETE) displayed suppressed TGF-β1-stimulated α-smooth muscle actin protein expression. These effects were suppressed in the presence of an inhibitor of a cytochrome P450 involved in EPA metabolism. This observation suggests that the EPA metabolites have antifibrotic effects. ω3PUFAs prevents AKI to CKD and renal fibrosis. Moreover, the EPA metabolites 18-HEPE, 17,18-EpETE and 17,18-diHETE were found to have antifibrotic effects.