Excitotoxicity, caused by over-stimulation or dysregulation of ionotropic glutamate receptors (iGluRs), is a major pathological process directing neuronal death in both acute and chronic neurological disorders. The aberrantly stimulated iGluRs direct massive influx of calcium ions into the affected neurons, leading to changes in expression and phosphorylation levels of specific neuronal proteins to modulate their functions and direct their participation in signalling pathways that induce excitotoxic neuronal death. To define these pathways, herein we utilised quantitative proteomics and phosphoproteomics analysis and identified over 150 neuronal proteins with significant dynamic temporal changes in abundance and/or phosphorylation levels at different time points (5 min to 4 h) after glutamate over-stimulation. Bioinformatic analysis predict that many of them are components of signalling networks directing defective neuronal morphology and functions, also Akt, Gsk3, Cdk5, JNK, CK2, SGK1 are predicted as the potential upstream kinases phosphorylating some of these perturbed proteins. Biochemical analysis confirmed the findings of the proteomic analysis for Erk1/2, Gsk3 and Tau. We also defined >40 neuronal protein and phosphoprotein molecules including CK2 and AMPK that are downstream of GluN-2B containing extra-synaptic NMDA receptors. Our predicted signalling networks and signalling dynamics of neuronal protein kinases form the conceptual framework for future investigation to define the spatial and temporal organisation of cell signalling pathways governing neuronal death in excitotoxicity.