To explore the vitamin D levels of periodontitis patients in comparison with periodontally healthy ones, and to assess the influence of vitamin D supplementation as an adjunctive during nonsurgical periodontal treatment (NSPT). Five databases (Pubmed, Embase, Scholar, Web of Sciences, and Cochrane Library) were searched until May 2020. Mean difference (MD) meta-analysis with corresponding 95% confidence interval (95% CI) and sensitivity tests via meta-regression were used. We followed Strength of Recommendation Taxonomy (SORT) to appraise the strength and quality of the evidence. Sixteen articles were included, fourteen case-control and two intervention studies, all reporting 25-hydroxyvitamin D (25(OH)D) levels. Compared with the healthy controls, the circulating 25(OH)D levels were significantly lower in chronic periodontitis patients (pooled MD = −6.80, 95% CI: −10.59 to −3.02). Subgroup analysis revealed differences among 25(OH)D measurements, with liquid chromatography-mass spectrometry being the most homogeneous method (pooled MD = −2.05, 95% CI: −3.40 to −0.71). Salivary levels of 25(OH)D showed no differences between groups. Due to the low number of studies, conclusions on aggressive periodontitis and in the effect of vitamin D supplementation after NSPT were not possible to ascribe. Compared with healthy controls, 25(OH)D serum levels are significantly lower in chronic periodontitis patients, with an overall SORT A recommendation. Future studies are needed to clarify the effect of vitamin D supplementation and the biological mechanisms linking vitamin D to the periodontium.