Endothelial progenitor cells (EPCs) participate in endothelial regeneration. Previous studies link vitamin D deficiency, inflammatory cytokines, and cardiovascular disease (CVD) risk. This study evaluates the impact of vitamin D supplementation on EPCs, inflammatory markers, and glycemia in type 2 diabetes. This is prospective open-label randomized controlled study. Sixty-five patients with type 2 diabetes, dyslipidemia, HbA1c below 9%, and vitamin D deficiency (below 30 ng/ml) attending the outpatient clinic between April and December 2015 were randomized to active vitamin D (60,000 IU of vitamin D orally once a week for 8 weeks, followed by once a month for 4 months) or control for 6 months. Data was analyzed with STATA 14. Demographics include median age 54 (range 48.5–60) years, median duration of diabetes 7 (4–12.5) years, mean BMI 26.86 ± 3.8 kg/m2, mean HbA1c 7.22±0.8%, and median vitamin D 13.42 (range 10.24–17.23) ng/ml; 50% were men. Vitamin D supplementation increased vitamin D levels in the active group compared to control (p < 0.01). EPCs decreased in both groups from baseline. There was no difference in change in EPCs, hsCRP, IL-6, IL-10, TNF-α, and HbA1c or insulin resistance (HOMA-IR) between the active- and control-groups at the end of the study. Vitamin D supplementation did not alter EPCs or inflammatory markers, or improve glycemic control at the dose and duration investigated. Further studies are needed to study the long-term effects on markers of endothelial repair.