Apert syndrome is characterized by craniosynostosis, midfacial hypoplasia and symmetric cutaneous and bony syndactyly of the limbs. The skull is usually hyperacrobrachycephalic, whereas frank cloverleafing, as a clinically obvious trilobed skull deformity, is rarely seen in these patients. We report a rare case of Apert syndrome with cloverleaf skull deformity, prenatally diagnosed at 26weeks’ gestation in which the sonographic features of a characteristic trilobed skull, abnormal biparietal diameter and head circumference, as well as malformations of the upper and lower extremities led to the diagnosis, confirmed by prenatal fibroblast growth factor receptor type 2 mutation analysis and fetal magnetic resonance imaging. The genetic evaluation revealed a p.P253R mutation in fibroblast growth factor receptor type 2 consisting in a transversion C>G at nucleotide 758. We discuss the relevant prenatal morphologic and genetic findings of this patient and review previously published cases. Our report demonstrates the feasibility of the prenatal diagnosis of Apert syndrome with cloverleaf skull using ultrasound, fetal magnetic resonance imaging and mutation analysis, and also highlights the importance of the biparietal diameter as an early predictor of growth restriction in severe craniosynostosis cases.