Obesity is associated with the production of pro-inflammatory cytokines and therefore can lead to worsening of allergic reactions. Thus, there is cross-talk between obesity and allergic reactions. In this study, we investigated whether the anti-obesity action of fish oil supplementation is involved in the anti-allergic action also induced by fish oil. We observed attenuation of cedar pollen-induced IgE serum increases in two experimental protocols: 15% fish oil supplementation for 8 weeks, which attenuated body weight increases compared with 15% soybean supplementation, and 4% fish oil supplementation for 2 weeks, which did not affect body weight increases compared with 4% soybean or 4% lard supplementation. The former but not the latter protocol attenuated sneezing after pollen challenge. Gene expression of TNF-α and IL-13, a Th2 cytokine, was moderately reduced in the trachea and nasal mucosa in mice fed fish oil supplements. In a third protocol, fish oil was administered for up to 15 weeks after a cedar pollen sensitization and challenge-induced increase in IgE levels. These levels decreased following fish oil supplementation but were almost unaffected by soybean oil supplementation. Surprisingly, the IL-13 gene expression level in the nasal mucosa and trachea was higher in the fish oil group than in the soybean oil group. These results suggest that fish oil supplementation before, during, or after antigen sensitization and challenge in mice helped to reduce cedar pollen-induced allergic reactions independent of its anti-obesity action. Fish oil supplementation can also exhibit pro-or anti-inflammatory action against IL-13 expression depending on the experimental protocol.