Probiotics are being used increasingly in pregnant women, whereas the efficiency on pregnancy outcomes is yet lacking. The meta-analysis was conducted to investigate the effectiveness of probiotic supplementation in pregnant women based on published randomized controlled trials (RCTs). PubMed, Embase, and the Cochrane library were searched throughout August 2018 to select the RCTs focused on the effectiveness of probiotic supplementation in pregnant women. Relative risks or weighted mean differences with 95% confidence intervals were employed to calculate the summary outcomes. A total of 18 RCTs including 4,356 pregnant women were eligible. The summary RRs indicated that probiotic supplementation was associated with a significant decrease in the risk of atopic eczema (RR: 0.68; 95% CI: 0.58–0.81; P<0.001) and eczema (RR: 0.79; 95% CI: 0.68–0.91; P=0.002) without significant heterogeneity. No significant differences were detected between probiotic and placebo for the incidence of allergic disease (P=0.303), IgE-associated allergic disease (P=0.946), asthma (P=0.501), sensitization (P=0.082), and cesarean section (P=0.091). Probiotic supplementation was associated with a prolonged gestational age (WMD: 0.09; 95% CI: 0.04–0.15; P=0.001) with insignificant heterogeneity, whereas no significant effect was exerted on birth weight (P=0.851). The risk of death (RR: 0.34; 95% CI: 0.13–0.91; P=0.031) and necrotizing enterocolitis (RR: 0.38; 95% CI: 0.18–0.81; P=0.012) was significantly reduced in pregnant women receiving probiotics without evidence of heterogeneity, while the risk of gastrointestinal symptoms (P=0.350), preeclampsia (P=0.165), and sepsis (P=0.532) was not statistically significant. These findings suggested that probiotics in pregnant women were beneficial for atopic eczema, eczema, gestational age, death, and necrotizing enterocolitis.