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The evolutionary trajectory of glioblastoma (GBM) is a multifaceted biological process that extends beyond genetic alterations alone. Here, we perform an integrative proteogenomic analysis of 123 longitudinal glioblastoma pairs and identify a highly proliferative cellular state at diagnosis and replacement by activation of neuronal transition and synaptogenic pathways in recurrent tumors. Proteomic and phosphoproteomic analyses reveal that the molecular transition to neuronal state at recurrence is marked by post-translational activation of the wingless-related integration site (WNT)/ planar cell polarity (PCP) signaling pathway and BRAF protein kinase. Consistently, multi-omic analysis of patient-derived xenograft (PDX) models mirror similar patterns of evolutionary trajectory. Inhibition of B-raf proto-oncogene (BRAF) kinase impairs both neuronal transition and migration capability of recurrent tumor cells, phenotypic hallmarks of post-therapy progression. Combinatorial treatment of temozolomide (TMZ) with BRAF inhibitor, vemurafenib, significantly extends the survival of PDX models. This study provides comprehensive insights into the biological mechanisms of glioblastoma evolution and treatment resistance, highlighting promising therapeutic strategies for clinical intervention. [Display omitted] • Longitudinal proteogenomic analysis reveals increased neuronal state at recurrence • Neuronal transition associates with activation of WNT/PCP pathway and BRAF kinase • Resistance to therapy via neuronal transition is recapitulated in GBM PDX models • BRAF kinase inhibition impairs the neuronal transition of GBM at recurrence Kim et al. reveal that glioblastoma develops therapeutic resistance through a neuronal transition caused by changes in the WNT/PCP pathway and BRAF kinase, as shown by extensive proteogenomic analysis. Notably, inhibiting BRAF kinase disrupts this lethal transformation, offering potential therapeutic avenues. [ABSTRACT FROM AUTHOR]