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Abstract Background Vitamin D is involved in the host immune response toward Mycobacterium tuberculosis. However, the efficacy of vitamin D supplementation on sputum conversion, clinical response to treatment, adverse events, and mortality in patients with pulmonary tuberculosis (PTB) remains controversial. We aimed to clarify the efficacy and safety of vitamin D supplementation in PTB treatment. Methods We searched Medline, Embase, Cochrane Central Register of Controlled Trials, Web of Science for double-blind, randomized controlled trials of vitamin D supplementation in patients with PTB that reported sputum conversion, clinical response to treatment, adverse events, or mortality, published from database inception to November 26, 2017. This study was registered with PROSPERO, number CRD42018081236. Results A total of 1787 patients with active PTB receiving vitamin D supplementation along with standard anti-tuberculosis regimen were included in the eight trials with different doses of vitamin D ranging from 1000 IU/day to 600,000 IU/month at different intervals. Primary analysis revealed that vitamin D supplementation increased the proportion of sputum smear and culture conversions (OR 1.21, 95%CI 1.05~ 1.39, z = 2.69, P = 0.007; OR 1.22, 95%CI 1.04~ 1.43, z = 2.41, P = 0.02), but did not improve the time to sputum smear and culture conversions (HR 1.07, 95%CI 0.83~ 1.37, z = 0.50, P = 0.62; HR 0.97, 95%CI 0.76~ 1.23, z = 0.29, P = 0.77). In the secondary analysis, vitamin D improved serum 25(OH)D, plasma calcium concentration, lymphocyte count, and chest radiograph (MD 103.36, 95%CI 84.20~ 122.53, z = 10.57, P < 0.00001; SMD 0.26, 95%CI 0.15~ 0.37, z = 4.61, P < 0.00001; MD 0.09, 95%CI 0.03~ 0.14, z = 2.94, P = 0.003); MD -0.33, 95% CI -0.57~ − 0.08 z = 2.57, P = 0.01), but had no impact on adverse events, mortality and other indicators(TB score, BMI, mean mid-upper arm circumference, weight gain, CRP, ESR, and other blood cells) (P > 0.05). Conclusions Vitamin D supplementation can be considered as a combination therapy in patients with PTB.