Background: MicroRNAs have recently been introduced as epigenetic regulators of glucose and lipid metabolic pathways, which are impaired in obesity and diabetes. Objectives: We evaluated the effects of calorie-restricted diet therapy on the circulating levels of miR-33b and miR-29a in relationship to glucose and lipid metabolic parameters in obese patients with type 2 diabetes mellitus (T2DM). Methods: This randomized clinical controlled trial was performed on 30 eligible obese women with T2DM, randomly divided into two groups (control group, n = 15; diet therapy group, n = 15) for 10 weeks. Ten healthy women with normal weight were enrolled at the baseline of the study as controls. Demographic information, dietary intake, and anthropometric and biochemical indices were obtained before and after the study. Circulating miR-33b and miR-29a were assessed for all subjects using quantitative RT-PCR, and the fold change of each circulating miRNA was compared between groups. Results: The circulating levels of miR-29a and miR-33b in the diabetic women were higher (0.40-fold) and lower (1.43-fold), respectively, than normal levels. Diet therapy significantly increased the circulating level of miR-33b (P = 0.023, 0.97-fold upregulation) to normal levels. This increase was independently correlated with caloric restriction (95%CI: -0.004 to -0.0001, P = 0.022) and 2hPPBS (95%CI: -0.009 to -0.001, P = 0.035). No remarkable change was observed in circulating levels of miR-29a. Conclusions: Our findings introduced a novel therapeutic effect of diet therapy on circulating miRNAs in obese patients with T2DM. MiR-33b is an important therapeutic target in the treatment and prevention of T2DM and its complications.