This metabolite dataset was collected from transgenic murine retinal ganglion cells (RGC) expressing bacterial channelrhodopsin labeled with fluorescent protein. Mice were subjected to optic nerve crush (ONC) with subsequent RGC stimulation of channelrhodopsin with blue light (promoting regeneration) or non-stimulation (control). ONC induces retinal ganglion cell degeneration over time with progressive loss of axons. In transgenic bacterial channelrhodopsin expressing RGC cells, light stimulation promotes regeneration of ONC axons. Genetically matched wild-type uninjured optic nerves were analyzed as controls for comparison. Metabolites were carefully extracted from finely minced optic nerve tissue using a solvent system (initial separation using 1:1 methanol and H2O and second extraction using 8:1:1 of acetonitrile:acetone:methanol). Untargeted liquid chromatography-mass spectrometry profiling was performed using fractionation on a Vanquish Horizon Binary UHPLC. Subsequent analyses were performed on an inline coupled Q-Exactive Orbitrap instrument. Metabolites were identified using Compound DiscovererTM software. Statistical analysis was performed using MetaboAnalyst 5.0. This data is available on Metabolomics Workbench, Study ID ST002111.