Narcolepsy type 1 (NT1) is a rare and life-long disease, characterized by central hypersomnia and cataplexy typically triggered by emotions. NT1 is linked to a selective loss of hypothalamic hypocretin neurons. To characterise neurodegeneration, we combined pons 1H-MRS and whole brain structural analysis in a large and homogenous sample of adult NT1 patients. 1H-MRS showed evidence of pontine neuronal dysfunction, consistent with its key role in REM sleep regulation. Grey matter loss was detected in brain regions implicated in the disease pathophysiology, including frontal-prefrontal cortices, putamen nuclei, thalami, hypothalamus, amygdalae, cerebellum, and widespread subtle tissue microstructural alterations were also found.