Because the differentiation between phenotypic expansion and blended phenotypes is not clear, the mixed phenotypes of blended rare genetic diseases make diagnosis difficult. We describe a family with the co-existence and co-segregation of generalized epilepsy with febrile seizures plus (GEFS+) and Kabuki syndrome (KS). The proband, a 7-year-old male, presented with GEFS+, dysmorphic facial features, short stature, developmental delay, and intellectual disability. Two novel missense mutations: p.G325A in the KDM6A gene responsible for KS and p.G1877V in the SCN1A gene responsible for GEFS+ were identified using the TruSight One sequencing panel. This family is the first in the literature to be confirmed molecularly with the blended phenotype of GEFS+ and KS. Furthermore, two affected female patients with X-linked KS showed a partial escape X-inactivation pattern of KDM6A with milder phenotypes than the male affected proband in this study.