The aim of the current study was to describe the magnitude and pattern of congenital anomalies on routine second-trimester ultrasound and its practical implication in the management of pregnant women with fetal anomalies at a novice center in East Africa. This cross-sectional study was conducted from September 2021 to May 2022 among women who had second-trimester anatomic scanning. Data were collected using a structured questionnaire and analyzed using SPSS version 23.1. Ethical clearance was obtained from the hospital's institutional review board and informed consent was obtained. The number of congenital anomalies was 45 of 1764 (2.55%). Most (41%) were in the age group 26-30 years and multigravida (62%). Average gestational age at anatomic scanning was 24 weeks. One or more risk factors for congenital anomalies were reported in 19 (31.0%) of the mothers. Most sonographic fetal abnormalities (51.7%) were reported in the central nervous system, followed by renal (18.0%) and skeletal (11.5%). Among the central nervous system anomalies, severe ventriculomegaly was the most common (38.7%), followed by Arnold-Chiari malformation (19.4%). Thirty-five (2%) of the mothers had a lethal fetal congenital anomaly and their pregnancy was terminated after counseling and informed consent. The rate of congenital anomalies in this study is comparable with most international data. The introduction of second-trimester anatomic scanning has led to timely termination of anomalous pregnancies, which contributes to reduction in direct and indirect costs of care and family's psychosocial distress and the stigma associated with the birth of and caring for a child with disability.