AbstractDisability worsening in multiple sclerosis (MS) is linked to neurodegeneration. Cholesterol homeostasis is essential for normal brain function. CYP46A1, crucial for brain cholesterol turnover and reduced in some neurodegenerative diseases, is a potential neuroprotective target. We hypothesized that CYP46A1 is downregulated in MS brains and linked to cholesterol dysbalance. Mass spectrometric analysis of sterols was performed from matched plasma and cerebrospinal fluid (CSF) in an all‐female MS cohort (n = 32, mean age = 33). Disability status was recorded at baseline and follow‐up. MS brain tissue samples (n = 11; 7 females; ages 38–67; 10 Secondary Progressive MS, 1 Primary Progressive MS; Disease Duration: 13–49 years) and control samples (n = 8; 3 females; ages 41–68) analysed for pathological regions using mass spectrometry and RNA expression using in‐situ hybridization. Significant dysregulation in 25‐hydroxycholesterol, 27‐hydroxycholesterol and 3β‐hydroxycholestenoic acid in CSF correlated with disability at baseline and follow‐up in the patient population. In brain tissue, reduced cholesterol, 24S‐hydroxycholesterol and 24S,25‐epoxycholesterol were observed in white matter lesions (p < 0.05), linked to CYP46A1 activity. CYP46A1 expression was enriched in neurons, with reductions in MS grey matter lesions and non‐lesions compared to controls (p < 0.01). Cholesterol metabolism is dysregulated in MS and is associated with reduced neuron‐specific CYP46A1 expression. Modulating CYP46A1, a druggable target, may benefit progressive MS.