Joubert syndrome (JBTS) is a clinically and genetically heterogeneous group of ciliopathy with a key diagnostic feature of ‘molar tooth sign’ in brain MRI. So far, over 20 causative genes have been identified, but only one gene (OFD1) results in X-linked Joubert syndrome 10 (JBTS10). Six mutations in the OFD1 gene have been found to cause JBTS10. In this study, we identified a novel OFD1 mutation of c.2843_2844 delAA (p.Lys948ArgfsX) in a 3-month-old boy with a ‘molar tooth sign’ and clinical features of JBTS using targeted exome next-generation sequencing. The de-novo OFD1 mutation in exon 21 leads to a frameshift mutation generating a prematurely truncated protein and is predicted to partly reduce the function of the OFD1 protein. Our study expands the genotype–phenotype spectrum in JBTS and will have applications in prenatal and early diagnosis of the disorder. This is the first report of the OFD1 mutation causing JBTS in a Chinese population.