Point mutations in the human BRAF gene are associated with a group of heterogeneous autosomal dominant neuro-cardio-facial-cutaneous syndromes. We identified a novel 93 kb intragenic deletion of the BRAF gene in a boy with severe developmental encephalopathy using microarray-based comparative genomic hybridization. The unique genotype and phenotype in this patient expands the spectrum of BRAF-related neurodevelopmental disorders. We propose a BRAF gene loss-of-function mechanism to best explain the biological basis of this severe developmental encephalopathy with postnatal growth deficiency.