Background: Coronavirus disease 2019 (COVID-19) can cause pulmonary and systemic inflammation in both children and adults. Investigating the potential impact of micronutrient deficiencies on COVID-19 infection is of great importance. Objectives: This case-control study was designed to compare the serum levels of vitamins D and C and zinc between healthy children and children with mild or severe COVID-19 infection, as well as to investigate the impact of micronutrient deficiencies on the clinical symptoms of patients. Methods: This case-control study was conducted at a teaching hospital in Tehran, Iran. Control subjects were recruited from healthy children, and cases were included from children with mild and severe symptoms of COVID-19. Blood samples were obtained from participants to measure the levels of micronutrients and were analyzed using statistical software. Results: A total of 85 subjects were included (33 controls, 25 cases with mild symptoms, and 27 cases with severe symptoms). We found no differences in the means of serum vitamin D and vitamin C levels between the studied groups. However, the mean serum zinc level was significantly lower in severe patients compared to the controls (P < 0.01). Moreover, no significant difference was observed in the frequency of patients with micronutrient deficiencies based on their clinical conditions. Conclusions: Our findings revealed zinc deficiency in children with severe COVID-19 infection, while no significant differences were found in the mean serum levels of vitamins D and C between healthy children and patients. More studies are necessary to provide more robust evidence.