Background Severe coronavirus disease 2019 (COVID-19) infections are associated with increased levels of C-reactive protein (CRP) and several pro-inflammatory cytokines leading to cytokine storm. Vitamin D has been proved to be associated with biological activities of the innate and adaptive immune systems. There is a growing number of data showing an association between serum vitamin D level and the different clinical outcomes of COVID-19 infection. Our aim is to evaluate the relation between serum vitamin D levels and the severity and mortality of COVID-19 infection in an Egyptian cohort. Results The study included 80 COVID-19 patients, 38 males (47.5%) and 42 females (52.5%), with a mean age of 52 ± 11.4 years (18–80 years). The serum vitamin D levels ranged between 2 and 30 ng/mL with a mean of 12.05 ± 9.04. Patients who were intubated had the lowest levels of serum vitamin D (7.26 ng/ml ± 5.21), while patients who had no need for oxygen supply had the highest levels (20.00 ng/ml ± 9.23) (P = 0.025). A highly significant negative correlation was found between serum vitamin D level and each of CRP and serum ferritin (r = − 0.346 and − 0.313) (P = 0.002 and 0.005). Of the enrolled 80 patients, 63 (79%) recovered (group 1) and 17 (21%) died (group 2). Group 2 had significantly lower vitamin D levels (6.17 ng/mL ± 3.22) and hemoglobin (10.75 ± 1.74) than group 1 patients (13.63ng/mL ± 9.46) (12.10 ± 1.85) (P = 0.002 and 0.009 respectively). Conclusion Serum vitamin D levels are significantly lower in patients needing mechanical ventilation, and in deceased patients, and are inversely related to the inflammatory markers CRP and serum ferritin, suggesting a relation between vitamin D insufficiency and poor COVID-19 outcome.