Background: Congenital anomalies are among the leading causes of fetal loss, despite it can be identified prior to birth through advanced technology in expert hands. Our research aimed at estimating the prevalence of congenital anomalies in Sudan. Methods: A facility-based retrospective cross-sectional study combined with a community-based survey through a telephone interview was implemented on a purposive convenient sample of 138 participants. The data were computerized in Epi Info 7. Google Earth Pro enabled to collect the geographical coordinates for the residence of the participants. Descriptive statistics were performed through SPSS 23 and ArcGIS 10.3 was used to generate the geographical distribution map of congenital defects to visualize the catchment areas of Soba Ultrasonography Unit. Results: Of the 138 participants, the estimated prevalence of congenital defects was 2.2/10,000 live births. The ultrasonography screening revealed that neural tube defects were the most prevalent anomalies with 13.0% (18/138), which represented 47.4% (18/38) of all defects. Concerning children, a mortality rate of 23.2% (32/138) was reported. Conclusions: The child mortality rate post ultrasound screening of 23.2%, and the neural tube defects being the most common anomalies appealed to Sudan health authorities for focusing on more preventive antenatal practices to strengthen and promote maternal and child health.