Chronic granulomatous disease (CGD) is a rare inherited immunodeficiency that arises from defects in the NADPH oxidase complex, primarily affecting the respiratory burst in neutrophils. Kabuki syndrome (KS) is a rare genetic syndrome and often present with facial, skeletal, visceral and cardiac anomalies, immunological defects and varying degrees of mental retardation. A 20-year-old male was admitted with the complaints of the recurrent abscess. He had a history of recurrent abscesses and long-term antituberculosis treatment. Cytometric functional analysis, Sanger sequencing and whole-exome sequencing were used for the diagnosis of CGD. Both AR-CGD (p67phox defect) with homozygous c.229C>T nonsense mutation in NCF2 gene and heterozygous nucleotide change c.3983G>A in the KMT2D gene causing a novel missense mutation p. Arg1328Gln resulted in Kabuki syndrome. To our knowledge, this is the first report of both CGD and Kabuki syndrome combined in a single patient. CGD is always considered for the differential diagnosis during BCGitis history and recurrent skin abscess.