Purpose The purpose of this double-blind, placebo-controlled study was to examine the effect of two fish oil supplements, one high in EPA (750 mg EPA, 50 mg DHA) and one low in EPA (150 mg EPA, 100 mg DHA), taken acutely as a recovery strategy following EIMD. Methods Twenty-seven physically active males (26 ± 4 year, 1.77 ± 0.07 m, 80 ± 10 kg) completed 100 plyometric drop jumps to induce muscle damage. Perceptual (perceived soreness) and functional (isokinetic muscle strength at 60° and 180° s−1, squat jump performance and countermovement jump performance) indices of EIMD were recorded before, and 1, 24, 48, 72, and 96h after the damaging protocol. Immediately after the damaging protocol, volunteers ingested either a placebo (Con), a low-EPA fish oil (Low EPA) or a high-EPA fish oil (High EPA) at a dose of 1 g per 10 kg body mass. Results A significant group main effect was observed for squat jump, with the High EPA group performing better than Con and Low EPA groups (average performance decrement, 2.1, 8.3 and 9.8%, respectively), and similar findings were observed for countermovement jump performance, (average performance decrement, 1.7, 6.8 and 6.8%, respectively, p = 0.07). Significant time, but no interaction main effects were observed for all functional and perceptual indices measured, although large effect sizes demonstrate a possible ameliorating effect of high dose of EPA fish supplementation (effect sizes ≥0.14). Conclusion This study indicates that an acute dose of high-EPA fish oil may ameliorate the functional changes following EIMD.