Mutations in the UGT1A1 gene cause Crigler-Najjar syndrome (CN), which causes non-hemolytic unconjugated hyperbilirubinemia, and is categorized as CN1 and CN2 according to the severity of bilirubin levels. The UGT1A1 gene is responsible for encoding the liver enzyme uridine diphosphate-glucuronosyltransferase, UGT1A1. This protein adds glucuronic acid to unconjugated bilirubin in bilirubin metabolism to form conjugated bilirubin. CN2 occurs when UGT1A1 activity is low, while CN1 is the absence of UGT1A1 activity; therefore, the CN2 phenotype is not as severe as that of CN1. Here, we report a novel allele of compound heterozygous mutations in UGT1A1 in a Thai male infant with clinical symptoms of CN2. The patient's compound heterozygosity was composed of a novel mutation, c.1069-1070insC, and the c.1456T>G mutation. The novel c.1069-1070insC mutation generated a premature stop codon in exon 4 (p.R357Pfs*24). The healthy parents were heterozygous for the c.1069-1070insC mutation (father) and c.1456T>G missense mutation (mother). Our results suggest that compound heterozygosity of the novel c.1069-1070insC and c.1456T>G (c211 G >A) missense mutation in the UGT1A1 gene played a primary role in the development of CN2 unconjugated hyperbilirubinemia.