The association between serum vitamin D levels and urinary tract infection (UTI) in children is unclear. We undertook a systematic review and meta-analysis to evaluate the relationships between different vitamin D levels and the likelihood of UTI in children. Online databases, including Web of Science, PubMed, Embase, and Cochrane Library, were searched up to 6 February 2023 for studies based on the inclusion criteria. Weighted mean difference (WMD) and Odds Ratios (ORs), along with their 95% confidence intervals (CI), were calculated, and the random-effects model was used for analysis. Twelve case–control studies and one cross-sectional study (839 children with UTI and 929 controls) were included. We found that children with UTI had lower levels of serum vitamin D than healthy controls (WMD: −7.730, 95% CI: −11.57, −3.89; p < 0.001). Low vitamin D levels were significantly associated with UTI in children (OR: 2.80; 95% CI: 1.55, 5.05; p = 0.001). The likelihood of children having a UTI significantly increased when their serum vitamin D level was less than 20 ng/mL (OR: 5.49, 95% CI: 1.12, 27.04; p = 0.036). Therefore, vitamin D level, especially when less than 20 ng/mL, is a risk factor in UTI.