Background Women with GDM have a higher risk of future cardiovascular diseases (CVD). Meanwhile, synbiotics have been demonstrated to have favorable impacts on atherogenic indices, and inflammatory and oxidative stress indicators, all of which are known to be CVD-predictive factors. The aim of this randomized controlled trial was to evaluate the effects of synbiotic supplementation on the atherogenic indices of plasma, high-sensitivity C-reactive protein (hs-CRP), and plasma malondialdehyde (MDA) in women with GDM. Methods Eligible pregnant women with GDM were randomized into two groups to receive a daily synbiotic capsule [500 mg of L.acidophilus(5 × 1010 CFU/g), L.plantarum(1.5 × 1010 CFU/g), L.fermentum(7 × 109 CFU/g), L.Gasseri(2 × 1010 CFU/g) and 38.5 mg of fructo-oligo-saccharides], or placebo, for 6 weeks. The ratios of TC/HDL-C, LDL/HDL-C, and logTG/HDL-C were calculated as the atherogenic indices. Serum hs-CRP and MDA concentrations were quantified before and after the intervention. Cohen’s d(d) was used to calculate the magnitude of the effect. Results Ninety participants completed the study. There was no significant difference in dietary antioxidant and mineral intakes between the two groups. Compared with placebo, synbiotic supplementation resulted in a significant decrease in logTG/HDL-C ratio with a medium–low effect size (mean difference = −0.11; 95% CI −0.21, 0; P values for the placebo and the intervention groups were 0.02, and 0.042, respectively; P between groups = 0.003; d = 0.25). No significant changes were observed in other parameters. Conclusions Overall, 6 weeks of synbiotic supplementation in women with GDM resulted in a significant improvement in logTG/HDL-C, suggesting that synbiotics may have a beneficial role in reducing the risk of future CVDs associated with GDM. Nevertheless, more studies are needed to confirm the veracity of these results. Trial Registration IRCT201511183140N16 (December 29th, 2015).