Background The contribution of vitamin D to thyroid disorders has received paramount attention; however, results are mixed. Hence, we designed a systematic review and meta-analysis to obtain a definitive conclusion. Methods The search included PubMed, ISI Web of Science, Scopus, and Google Scholar databases up to March 2021 to collect available papers reporting the relationship between serum levels of vitamin D and thyroid disorders. The pooled effect was reported as weighted mean difference (WMD) and 95% confidence interval (CI). Results Out of 6123 datasets, 42 were eligible to get into this systematic review and meta-analysis. Serum vitamin D was markedly lower in autoimmune thyroid diseases (AITD) (WMD − 3.1 ng/dl; 95% CI, − 5.57 to − 0.66; P = 0.013; I2 = 99.9%), Hashimoto’s thyroiditis (HT) (WMD − 6.05 ng/dl; 95% CI, − 8.35 to − 3.75; P < 0.001; I2 = 91.0%) and hypothyroidism patients (WMD − 13.43 ng/dl; 95% CI, − 26.04 to − 0.81; P = 0.03; I2 = 99.5%), but not in subjects with Graves’ disease (GD) (WMD − 4.14 ng/dl; 95% CI, − 8.46 to 0.17; P = 0.06; I2 = 97.5%). Conclusions Our findings suggested lower vitamin D levels in patients with hypothyroidism, AITD, and HT compared to healthy subjects. However, the link between serum vitamin D and GD was only significant among subjects ≥40 years old.