Background: Neonatal sepsis is one of the most important causes of an infant’s death, and the identification of its factors has been the subject of many studies. Some new evidence suggested the role of vitamin D in the occurrence of sepsis in infants. Objectives: The aim of this study was to compare the serum levels of vitamin D in neonates with sepsis in the first week of birth and healthy neonates. Methods: This case-control study was performed on 72 term neonates (36 neonates with sepsis as the case and 36 healthy neonates as the control group) who referred to Bandar Abbas children's hospitals, Bandar Abbas, Iran, from 2016 - 2017. Results: Serum vitamin D levels were measured in all infants and their mothers in both sepsis and control groups. In addition, data were collected, including sex, birth weight, C-reactive protein (CRP), and duration of hospitalization in neonates with sepsis. The mean serum level of vitamin D was 18.52 ± 11.49 ng/mL in sepsis and 20.52 ± 13.75 ng/mL in neonates of the control group (P ≥ 0.05). The mean maternal serum level of vitamin D in sepsis control groups was 22.44 ± 11.26 and 24.36 ± 12.82 ng/mL, respectively (P ≥ 0.05). There was a positive correlation between maternal and neonatal vitamin D levels in the sepsis (r = 0.803) and the control (r = 0.756) groups. However, there was no significant difference between vitamin D level and CRP (P = 0.148) and length of hospital stay (P = 0.396) in the sepsis group. Conclusions: Although the results of the present study showed a correlation between serum vitamin D levels in mothers and neonates with neonatal sepsis, there was no significant correlation between neonates with and without sepsis regarding vitamin D levels.