Background: Deficiencies in vitamin A and D are prevalent among pregnant women, which may further exacerbate anemia during pregnancy and diminish the health of the newborn. These lipophilic vitamins are essential for the formation of red blood cells and the transfer of fetal nutrients. The impact of vitamin A and D deficiencies on maternal and neonatal hemoglobin levels is of concern; however, it lacks comprehensive examination among various local populations. To evaluate the association between maternal vitamin A and D deficiency and hemoglobin concentration in mothers and their newborns. Methods: This cross-sectional study, conducted at Khyber Medical College and its affiliated hospital, lasted from January 2023 to January 2024. Ninety-seven pregnant women who delivered at term were enrolled. Blood samples from mothers and umbilical cords were taken to evaluate Vitamin A and D levels, serum levels, and hemoglobin concentrations. Sociodemographic, clinical, and other relevant data were also captured. Deficient and non deficient group comparisons were made using independent sample t-tests to ascertain the differences between the two groups' hemoglobin levels. Results: Vitamin A deficiency was identified in 36.1% of participants, while 43.3% were deficient in vitamin D. Maternal anemia was present in 42.3% of cases, and 37.1% of neonates had low hemoglobin levels. Women with vitamin A or D deficiency had significantly lower mean hemoglobin levels than normal (p < 0.05). A similar trend was observed in neonatal hemoglobin concentrations. Conclusion: Vitamin A and D deficiency during pregnancy are significantly associated with reduced hemoglobin levels in both mothers and their newborns. Early identification and correction of these deficiencies could help prevent maternal anemia and improve neonatal outcomes. Strengthening antenatal nutrition programs may be a practical approach to addressing this public health issue.