We report a case of fetal cerebellar vermis dysplasia diagnosed prenatally by ultrasonography. Ultrasonography of the 27-year-old woman at 20 +6 gestational weeks revealed partial separation of the cerebellar vermis (Dandy-Walker variants), unclosable upper and lower lips, and polydactyly, based on which a preliminary diagnosis of multiple fetal malformations was made. Karyotype and chromosomal microarray (CMA) analysis of the amniotic fluid showed no abnormality. After genetic counseling, amniocentesis was performed again for a whole-exome sequencing test. The results suggested that there are compound heterozygous variations of c.3435G>A(P.W1145X) and c.2941C>G(p. p981A) in the exon 19 and exon 17 of the CPLANE1 gene, which were both de novo mutations and inherited from the father and mother, respectively. The fetus was diagnosed as Joubert syndrome. Given the facial and limb deformities and a significant risk of neurological abnormalities of the fetus, the patient and her family decided to terminate the pregnancy.