Cerebral cavernous malformations (CCMs) are one of the most common types of vascular malformation, which are featured enlarged and irregular small blood vessels. The cavernous cavities are merely composed of a single layer of endothelial cells and lack other support tissues, such as elastic fibers and smooth muscle, which make them elastic. CCMs may develop in sporadic or familial forms with autosomal dominant inheritance. Mutations have been identified in three genes: KRIT1, MGC4607, and PDCD10. Here, we report a typical case of CCMs in a 44-year-old woman associated with a novel mutation in PDCD10 gene. The patient, diagnosed with CCMs, has been suffering from headache for several months. Analyses of the Whole Exome Sequencing revealed a novel disease-associated mutation in the already known disease-associated PDCD10 gene. This mutation consists a nucleotide deletion (c.212delG) within the exon 4, resulting in premature protein termination (p.S71Tfs*18). This novel mutation significantly enriches the spectrum of mutations responsible for CCMs, providing a new evidence for further clarifying the genotype-phenotype correlations in CCMs patients.