Vitamin D (VD) plays an important role in infectious and autoimmune diseases. We investigated the association between the serum VD levels and active human cytomegalovirus (HCMV) infections in pediatric systemic lupus erythematosus (SLE) patients. From January 2015 to June 2021, 120 children were diagnosed with SLE, and 100 healthy children were enrolled. The serum 25-hydroxyvitamin D [25(OH)D] levels were detected using ELISA. The serum anti-HCMV IgM antibodies were measured by a chemiluminescence immunoassay. Comparisons of the 25(OH)D levels between SLE patients and healthy children were performed, as well as subgroups of SLE patients with or without active HCMV infections. The serum 25(OH)D levels of SLE patients were significantly lower than those of healthy children (35.3 ± 12.9 vs. 49.3 ± 15.3, P < 0.001). The VD deficiency ratio was higher in SLE patients (89.2%) than that in healthy children (52.0%). The serum 25(OH)D levels in the positive anti-HCMV IgM group were significantly lower than those of the negative anti-HCMV IgM group (30.6 ± 12.3 vs. 38.2 ± 12.5, P < 0.001). A severe VD deficiency ratio was significantly higher in HCMV-IgM(+)-SLE patients (42.2%) than that in HCMV-IgM(−)-SLE patients (13.3%). This study suggested that the serum VD level is associated with active HCMV infections in pediatric SLE patients.