Gestational diabetes mellitus (GDM) affects 1%–14% of all gestations. The importance of GDM stems from its relationship with adverse pregnancy outcomes. This study aimed to evaluate the correlations of vitamin D receptor (VDR) gene FokI polymorphisms with GDM in the Egyptian population. In a comparative case-control study, 196 pregnant women were divided into GDM and control groups (98 each group). The VDR gene FokI genotypes were determined in pregnant women under investigation. Both groups show no statistically significant difference for serum 25-hydroxy vitamin D (25-OHD) level, maternal age, gestational age in weeks, parity, and blood pressure. On the other hand, past miscarriage history, body mass index (BMI), glycated hemoglobin (HbA1c), and homeostasis model assessment for insulin resistance (HOMA-IR) were significantly higher in the GDM group vs. the control group. Genotype CC was found as a risk factor for GDM due to the increased odds ratio (OR) 3.78 [(1.57–8.62)] (P = 0.002). The risk of GDM decreased significantly with the dominant homozygous allele T in the tested polymorphism TT + TC vs. CC (OR = 0.32, 95% CI = 0.15–0.68 and p-value = 0.002). Genotype CC is associated with vitamin D deficiency [OR 14.4 (4.03–51.5), P = 0.001], and C allele is also associated with vitamin D deficiency [OR 2.35 (1.28–4.30), P = 0.005)]. There was a relationship between VDR gene FokI polymorphism and the development of GDM. Besides, a possible association exists between genotype CC and C allele and vitamin D deficiency.