n-3 Polyunsaturated fatty acids (PUFAs) have been suggested as a preventive or therapeutic strategy for autoimmune or inflammatory diseases via the modulation of the activation, differentiation, and effector functions of various immune cells, especially T cells and macrophages. Despite the importance of B cells in the pathogenesis of autoimmune diseases, few studies have demonstrated their effect on B cells. In this study, we investigated the possible effects of n-3 PUFAs on B cell activation, differentiation, and isotype switching in fat-1 transgenic mice, which can convert n-6 PUFAs to n-3 PUFAs via n-3 desaturase derived from Caenorhabditis elegans. Fat-1 mice were fed a corn oil-rich diet for at least 4 weeks to increase the probability of converting n-6 PUFAs to n-3 PUFAs. Splenic B cells were then isolated, followed by stimulation with Toll-like receptor 4 or B cell receptor (BCR). Our results showed that increased n-3 PUFA levels in B cells by fat-1 overexpression inhibited B cell proliferation, cytokine secretion, such as interleukin (IL)-6, IL-10, tumor necrosis factor-α, plasma cell differentiation, and Ig isotype switching/secretion. These effects are possibly due to the suppression of Syk, Src, and AKT activation in B cells from fat-1 mice, as well as NF-κB. Collectively, our results suggest that fat-1 expression attenuates B cell responses, and n-3 PUFA supplementation can be a possible strategy to treat pathological conditions in which B cells play a key role.