Objective: To present the usefulness of fetal magnetic resonance (MR) imaging for accurate diagnosis of Pfeiffer syndrome type II. Case and Methods: A 19-year-old woman was referred to us at 29 weeks of gestation for prenatal management of hydrocephalus. Ultrasonography of the fetus showed cloverleaf skull with dilated lateral ventricles, exophthalmos, macroglossia, and a single ventricle of the heart in addition to polyhydramnios. MR imaging was performed at 30 weeks of gestation and revealed cloverleaf skull, dilated lateral ventricles, and broad thumb. Fetal karyotyping indicated 46,XY, but DNA sequence analysis showed a single sequence variation (Nt 1198A>G) in the fibroblast growth factor receptor (FGFR) 2 gene (exon 10). On the basis of these findings, the baby was diagnosed in utero with Pfeiffer syndrome type II. Following counseling, the pregnancy was terminated because polyhydramnios made the patient’s symptoms more severe. The patient delivered her baby vaginally at 34 weeks of gestation. The baby’s birth weight was 2,298 g; the baby was declared dead at 25 min after birth. Conclusion: The detailed findings obtained by a combination of ultrasound that included three-dimensional and MR imaging and confirmation sought via molecular testing led to an accurate diagnosis of Pfeiffer syndrome type II in utero.