Plant homeodomain finger gene 6 (PHF6) is a highly conserved chromatin associated protein that is important for neurodevelopment and hematopoiesis. Inherited or de novo mutations in the PHF6 gene cause Börjeson–Forssman–Lehmann syndrome (BFLS), a rare X-linked neurodevelopmental and endocrine disorder. Patients with BFLS present with intellectual disability (ID), which affects cognitive functioning and adaptive behaviour. To progress our understanding of how PHF6 mutations affect the nervous system in BFLS, we studied the impact of deletion of the Phf6 gene on brain development in conditional PHF6 knock-out mouse tissues and primary cell cultures. We report the anatomical, cellular and molecular effects of loss of PHF6 on the brain. Histological and morphological analysis of the brains revealed differences in the size of the brain in adult Phf6 mutant mice compared to wild-type littermate controls. RNA-sequencing of the cortex and cortical neurons revealed transcriptional changes in various neuronal development and function processes in the mice with loss of PHF6. At the cellular level, proliferation and differentiation of neuronal cells were affected by loss of PHF6. Our data provide insight into development of the brain of the BFLS mice and the anatomical, cellular and molecular effects of loss of PHF6.