Benign familial neonatal convulsions (BFNC, also named benign familial neonatal seizures, BFNS) is a rare autosomal dominant inherited epilepsy syndrome with clinical and genetic heterogeneity. Two voltage-gated potassium channel subunit genes, KCNQ2 and KCNQ3, have been identified to cause BFNC1 and BFNC2, respectively. To date, only three mutations of KCNQ3, all located within exon 5, have been reported. By limited linkage analysis and mutation analysis of KCNQ3 in a Chinese family with BFNC, we identified a novel missense mutation of KCNQ3, c.988C>T located within exon 6. c.988C>T led to the substitution Cys for Arg in amino acid position 330 (p.R330C) in KCNQ3 potassium channel, which possibly impaired the neuronal M-current and altered neuronal excitability. Seizures of all BFNC patients started from day 2 to 3 after birth and remitted during 1 month, and no recurrence was found. One family member who displayed fever-associated seizures for two times at age 5 years and was diagnosed as febrile seizures, however, did not carry this mutation, which suggests that febrile seizures and BFNC have different pathogenesis. To our knowledge, this is the first report of KCNQ3 mutation in Chinese family with BFNC.