We investigated the effect of daily intake of yogurt drink fortified with either vitamin D alone or with added calcium on resting metabolic rate (RMR), thyroid hormones and homeostatic model assessment for insulin resistance in subjects with type 2 diabetes (T2D). A total of 75 adult subjects with T2D were randomly assigned to 1 of the 3 groups to receive either D-fortified yogurt drink (DY; 1000IU vitaminD/day), Ca-D-fortified yogurt drink (CDY; 1000IU vitamin D plus 500mg calcium), or plain yogurt drink for 12 weeks. All assessments were done at the baseline and after the intervention. The concentrations of anti-thyroid peroxidase antibody (anti-TPO-Ab), intact parathyroid hormone (iPTH) and thyroid stimulating hormone (TSH) had declined significantly compared with baseline values only in the CDY group. The mean RMR increased in both DY and CDY groups (p< 0.001 for both). Also, changes of serum concentrations of 25-hydroxycalciferol (B= 2.96, 95% confidence interval (CI)= 1.3 to 4.6, p= 0.001) and iPTH (B= -2.41, 95%CI= -4.5 to -0.31, p= 0.025) remained significant predictors of RMR changes even after adjustment for changes of serum concentrations of TSH (B= -18.2, 95% CI= -61.7 to 25.2, p= 0.406). Daily intake of vitamin D together with calcium at physiological doses has attenuating effect on anti-TPO-Ab and TSH. Also, vitamin D with or without added calcium causes a significant thyroid-independent increase in RMR in euthyroid subjects with T2D. Registered at clinicaltrials.gov as NCT01229891. Novelty: Daily intake of vitamin D with calcium at physiological doses has attenuating effect on anti-TPO-Ab and TSH. Vitamin D with or without added calcium causes a thyroid-independent increase in RMR in euthyroid subjects with T2D.