Congenital malformations are defined as single or multiple defects of the morphogenesis of organs or body parts, identifiable during intrauterine life or at birth. With recent advances in prenatal detection of congenital malformations, many of these disorders can be identified early on a routine fetal ultrasound. The aim of the present systematic review is to systematize the current knowledge about the mode of delivery in pregnancies complicated by fetal anomalies. The databases Medline and Ebsco were searched from 2002 to 2022. The inclusion criteria were prenatally diagnosed fetal malformation, singleton pregnancy, and known delivery mode. After the first round of research, 546 studies were found. For further analysis, studies with full text available concerning human single pregnancy with known neonatal outcomes were considered. Publications were divided into six groups: congenital heart defects, neural tube defects, gastroschisis, fetal tumors, microcephaly, and lung and thorax malformations. Eighteen articles with a descripted delivery mode and neonatal outcome were chosen for further analysis. In most pregnancies complicated by the presence of fetal anomalies, spontaneous vaginal delivery should be a primary option, as it is associated with lower maternal morbidity and mortality. Cesarean delivery is generally indicated if a fetal anomaly is associated with the risk of dystocia, bleeding, or disruption of a protective sac; examples of such anomalies include giant omphaloceles, severe hydrocephalus, and large myelomeningocele and teratomas. Fetal anatomy ultrasound should be carried out early, leaving enough time to familiarize parents with all available options, including pregnancy termination, if an anomaly is detected.