Optical coherence tomography (OCT) is a non-invasive, cost-efficient technique that provides high-resolution in vivo imaging of retinal tissue. The peripapillary retinal nerve fibre layer (pRNFL) and macular ganglion cell complex (mGCC) are surrogate markers of neuroaxonal integrity in not only the eye, but also the central nervous system. Retinal atrophy may occur in tandem with central nervous system pathologies as a result of injury to ganglion cells, direct degeneration of the pregeniculate pathway, or retrograde transsynaptic degeneration secondary to postgeniculate lesions. In this review, we outline the basic principles of OCT and discuss its application to managing patients with demyelinating disorders, idiopathic intracranial hypertension, stroke, neurodegenerative conditions, and mitochondrial disorders. We demonstrate that measurements of pRNFL and mGCC thickness are paramount in diagnosing and monitoring neurologic disorders, including those with subclinical disease progression.