Background: Influence of fish oil supplementation on postoperative atrial fibrillation (POAF) was inconsistent according to published clinical trials. The aim of the meta-analysis was to evaluate the effects of perioperative fish oil supplementation on the incidence of POAF after cardiac surgery. Methods: Pubmed, Embase and the Cochrane Library databases were searched. Randomized controlled trials (RCTs) assessing perioperative fish oil supplementation for patients undergoing cardiac surgery were identified. Data concerning study design, patient characteristics, and outcomes were extracted. Risk ratio (RR) and weighted mean differences (WMD) were calculated using fixed or random effects models. Results: Eight RCTs involving 2687 patients were included. Perioperative supplementation of fish oil did not significantly reduce the incidence of POAF (RR = 0.86, 95% CI 0.71 to 1.03, p = 0.11) or length of hospitalization after surgery (WMD = 0.10 days, 95% CI: 0.48 to 0.67 days, p = 0.75). Fish oil supplementation also did not affect the perioperative mortality, incidence of major bleeding or the length of stay in the intensive care unit. Meta-regression and subgroup analyses indicated mean DHA dose in the supplements may be a potential modifier for the effects of fish oil for POAF. For supplements with DHA >1 g/d, fish oil significantly reduced the incidence of POAF; while it did not for the supplements with a lower dose of DHA. Conclusions: Current evidence did not support a preventative role of fish oil for POAF. However, relative amounts of DHA and EPA in fish oil may be important for the prevention of POAF.