Despite almost 25 years of fish oil supplementation (FS) research in athletes and widespread use by the athletic community, no systematic reviews of FS in athletes have been conducted. The objectives of the systematic review are to: 1) provide a summary of the effect of FS on the athlete’s physiology, health and performance; 2) report on the quality of the evidence; 3) document any side effects as reported in the athlete research; 4) discuss any risks associated with FS use; 5) provide guidance for FS use and highlight gaps for future research. Electronic databases (PubMed, EMBASE, Web of Science, Google Scholar) were searched up until April 2019. Only randomised placebo-controlled trials (RCTs) in athletes, assessing the effect of FS on a health, physiological/biochemical, or performance variable were included. Of the 137 papers identified through searches, 32 met inclusion criteria for final analysis. Athletes varied in classification from recreational to elite, and from Olympic to professional sports. Mean age for participants was 24.9 4.5 years, with 70% of RCTs in males. We report consistent effects for FS on reaction time, mood, cardiovascular dynamics in cyclists, skeletal muscle recovery, the pro-inflammatory cytokine TNF-alpha, and post-exercise nitric oxide responses. No clear effects on endurance performance, lung function, muscle force or training adaptation were evident. Methodological quality, applying the PEDro scale, ranged from 6 to a maximum of 11, with only four RCTs reporting effect sizes. Few negative outcomes were reported. We report various effects for FS on the athlete’s physiology; the most consistent findings were on the central nervous system, cardiovascular system, pro-inflammatory cytokines, and skeletal muscle. We provide recommendations for future research and discuss the potential risks with FS use.