A pilot study was done to assess whether synbiotics supplementation could optimize anthropometric indices in Iranian obese children. Participants included 46 overweight or obese children 7 to 13 years of age. The treatment group had a restricted diet, physical activity plan, and a synbiotics capsule per day for 12 weeks. The placebo group received a similar diet, activity plan, and placebo capsules. Body fat and z scores for body mass index showed significant reductions in both groups; however, waist circumference decreased significantly only in the synbiotics group. Between-group comparisons showed no significant differences in any variable. Our findings showed that synbiotics can improve the benefits of lifestyle modifications by decreasing waist circumference in overweight or obese children.