Background: Prediabetes is a high-risk condition for type 2 diabetes mellitus. The growing prevalence of diabetes emphasizes on the necessity of concentrating on various strategies to prediabetes prevention and management. Probiotics as a group of functional foods might exert antidiabetic effects. This study aimed to assess the effects of probiotic administration on blood lipid profile and blood pressure in patients with prediabetes. Methods: This randomized controlled trial consisted of 60 prediabetic patients, aged 25-65 years old, that were randomly assigned to the intervention (receiving 500 mg probiotic capsules, n = 30) or control group (receiving placebo, n = 30) for 8-week period. Demographic and anthropometric data were collected at baseline. Blood samples were collected at baseline and after 8 weeks for biochemical measurements. Blood pressure was measured at the baseline an after 8 weeks of intervention. Data regarding dietary intakes and physical activity were also collected during the study. We used SPSS software version 16 (SPSS Inc. Chicago, USA) for data analyzing. Results: Probiotic supplementation did not contribute to significant changes in total cholesterol, low-density lipoprotein (LDL)-cholesterol, high-density lipoprotein (HDL)-cholesterol, Triglycerides (TG), TG/LDL and LDL/HDL ratios, after 8 weeks. After adjusting for potential confounders, HDL-cholesterol reduced significantly in the placebo group compared with probiotic group. Percent change in systolic blood pressure was significantly different in the probiotic group in comparison with a placebo group (−3.10 ± 2.22 vs. 3.24 ± 1.96, P = 0.01), although this significance did not exist anymore after adjusting for confounders (P > 0.05). Conclusions: Our study showed that probiotics did not have significant effects on lipid markers although they had positive effects on systolic blood pressure.