Background: Pregnant women with pre-existing diabetes face an elevated risk of congenital anomalies in their offspring. However, research on the pattern of congenital anomalies and its correlation with blood sugar control in pre-gestational diabetic mothers is limited, especially in our country's context. This study investigated the association between elevated HbA1c levels and congenital anomalies in diabetes-related pregnancies. Objective: To assess whether raised HbA1c levels were linked to an increased incidence of congenitally deformed fetal outcomes in pregnancies affected by diabetes. Method: This cross-sectional study was conducted from August 2018 to September 2019 at the Department of Obstetrics and Gynaecology, DMCH. Women with pre-gestational diabetes were sequentially enrolled if they provided informed consent. Data, including HbA1c levels and anomaly scans, were collected at 18-24 weeks of gestation. Participants were divided into two groups based on HbA1c levels: Group-1 (elevated HbA1c) and Group-2 (normal HbA1c). Statistical analysis was performed using SPSS 22, with significance at p<0.05. Result: The mean ages of Group 1 and Group 2 were 31.60±2.89 & 30.51±2.99 (SD) years. Both groups were similar concerning age, residence, education, occupation, economic status, and BMI (p>0.05 in all factors). Mean HbA1C (%) of Group-1 and Group-2 were 8.57±2.22 & 6.18±0.20 (p<0.001), respectively. Congenital anomalies were more frequent in Group 1 (15.6 vs 2.2; p<0.05), and it is associated with high blood sugar levels (p<0.001) and with a previous history of anomalous babies in preceding pregnancies. Conclusion: Elevated HbA1c levels are associated with an increased incidence of congenital anomalies in pregnancies complicated by diabetes. This underscores the importance of strict glycemic control in pregnant women with pre-gestational diabetes to mitigate the risk of adverse fetal outcomes. Further, population-based studies are desired to validate these findings and inform clinical management strategies.