Pathogen infection stimulates the fatty acid (FA) metabolism and the production of pro-inflammatory derivatives of FA. Barramundi, Lates calcarifer, was fed on a diet rich in preformed long-chain (≥C20) polyunsaturated fatty acids (LC-PUFA) from fish oil (FO), to compare with diets containing high levels of C18 precursors for LC-PUFA - stearidonic (SDA) and γ-linolenic acid (GLA) - from Echium plantagineum (EO), or rapeseed oil (RO) rich in α-linolenic acid (ALA), but a poor source of LC-PUFA and their precursors. After 6 weeks, when growth rates were similar amongst the dietary treatments, a sub-lethal dose of Streptococcus iniae was administered to half of the fish, while the other half were maintained unchallenged and were pair-fed with the infected fish. Under a disease challenge situation, the tissue FA depots depleted at 3 days post-infection (DPI) and were then restored to their previous concentrations at 7 DPI. During the infection period, EO fish had a higher content of n3 and n6 PUFA in their tissues, higher n3:n6 PUFA ratio and reduced levels of the eicosanoids, TXB 2 and 6-keto-PGF1α, in their plasma compared with RO fish. Fish fed on FO and EO had a longer lasting and enduring response in their FA and eicosanoid concentrations, following a week of bacterial infection, compared with those fed on RO. EO, containing SDA and GLA and with a comparatively higher n3:n6 PUFA ratio, proved more effective than RO in compensating for immunity stress. © 2013 Elsevier Ltd.