This prospective study evaluated the short-term outcomes of 16 neonates undergoing single congenital omphalocele repair. Parents made informed choices for their baby to receive either immediate repair (IR group, n = 8) or repair ≥ 3 h after delivery (control group, n = 8). All babies were delivered by elective caesarian section. Babies in the two groups were matched one-to-one according to their birth weight, bulging volume and gestational age. Short-term outcomes included the incidence of infection and the lengths of stay in the neonatal intensive care unit (NICU) and in the hospital. Compared with the control group, the IR group showed a significantly lower incidence of infection, shorter surgical duration, shorter NICU stay, less time on total parenteral nutrition, less time to total enteral nutrition and shorter length of hospital stay. Immediate repair significantly improved the short-term neonatal outcomes of congenital omphalocele in China.