Growing evidence indicates that fish oil-containing lipid emulsions have a beneficial effect on parenteral nutrition-associated cholestasis (PNAC) in adults; however, data are limited in neonates regarding the effect of fish oil on PNAC. We conducted a meta-analysis of studies that addressed the effect of fish oil-containing lipid emulsions on reversing and preventing PNAC. We searched PubMed, the EMBASE database, and the Cochrane Library for this systematic review and meta-analysis. The methodologic assessment of studies was performed with the Jadad scale and the Newcastle-Ottawa Scale. Comprehensive Met-Analysis version 2.0 was used for the statistical analysis. We performed a meta-analysis with the primary outcomes of reversal of PNAC and the occurrence of PNAC in newborn infants, including preterm infants, after parenteral administration of fish oil-containing lipid emulsions. Of the 36 studies identified, 7 fulfilled the inclusion criteria and were used in this meta-analysis, including 3 studies with 93 participants in which reversal of PNAC was an outcome and 4 studies with 1012 participants on preventing PNAC. The use of fish oil-containing lipid emulsions was more likely to reverse PNAC (OR: 6.14; 95% CI: 2.27, 16.6; P < 0.01), but the use of fish oil-containing lipid emulsions did not have a significant effect on the development of PNAC (OR: 0.56; 95% CI: 0.28, 1.10; P = 0.09) compared with soybean-based or olive oil-based lipid emulsions. The pooled data suggest that the use of fish oil-containing lipid emulsions is effective for reversing PNAC but cannot prevent PNAC in neonates who require prolonged parenteral nutritional support.