Background: Congenital heart defects (CHDs) are among the most common birth disorders worldwide. Human research has produced mixed results regarding the impact of zinc on this population. Children with CHD often exhibit hyperparathyroidism and vitamin D deficiency. Objectives: This study aims to assess the levels of serum vitamin D and zinc in children with CHD and compare them to those of a control group. Methods: In this case-control study, we included children with CHD (N = 53) who were admitted to Bandar Abbas Children's Hospital from June 22 to December 21, 2018. The study's inclusion criteria were an age range from one month to 14 years and a CHD confirmation via echocardiography. A control group of children without CHD (n = 53) was also evaluated. We collected demographic information from participants and took 4cc blood samples from the children to measure their serum levels of vitamin D and zinc. Results: The study found no significant difference in serum vitamin D levels between the two groups (P = 0.242). However, the mean serum zinc level was significantly lower in CHD patients compared to the controls, indicating a moderate effect size (SMD = -0.67, 95% confidence interval [CI] -1.06 to -0.28). The frequency of deficiency and insufficiency in serum vitamin D levels was similar between both groups (P = 1.000 and P = 0.767, respectively). Nevertheless, CHD children were 4.31 times more likely to suffer from zinc deficiency than the control group (OR = 4.31, 95% CI 1.52 to 13.31). Moreover, a simultaneous insufficiency of zinc and vitamin D levels was observed exclusively in CHD children (P = 0.006). Conclusions: The study observed a zinc deficiency in children with CHD, while no significant differences were found in the deficiency and insufficiency of serum vitamin D levels between children with CHD and the control group. Future longitudinal studies are necessary to verify these findings.