It has been suggested that n-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs) have anti-inflammatory properties and may reduce the risk of allergic disease. Fish is a great source of n-3 LC-PUFAs. However, the effect of fish on allergic disease remains controversial. PubMed, EMBASE, and Cochrane Central Register of Controlled Trials were searched for randomized controlled trials (RCTs) and prospective cohort studies regarding the effect of fish intake during pregnancy or infancy on allergic outcomes in children. The outcomes of interest were atopy, eczema, allergic rhinitis, wheeze, asthma, and food allergy. One RCT and 17 publications from 13 prospective cohort studies were included for maternal fish intake during pregnancy, and eight publications from five prospective cohort studies for fish intake in infancy. Pooled analysis suggested that maternal fish intake during pregnancy was not associated with lower risk of any allergic outcome, both in RCT and observational studies. Consumption of fish during the first year of life reduced the risk of eczema (RR 0.61; 95% CI 0.47, 0.80; p = 0.0003; I²  = 68%) and allergic rhinitis (RR 0.54; 95% CI 0.36, 0.81; p = 0.003; I²  = 74%). Current evidence indicates that fish intake in infancy could reduce the risk of eczema and allergic rhinitis in children, whereas maternal fish intake during pregnancy does not affect any atopic outcome. The intake of fish per se in infancy, not specially n-3 LC-PUFAs, may have an allergy protective effect. High-quality and adequately powered RCTs are warranted to confirm this.