Purpose To investigate the associations between longitudinal changes in lipid biomarkers and serum neurofilament (sNfL) levels in multiple sclerosis (MS) neurodegeneration and disease progression. Methods 5-year prospective, longitudinal study included 75 relapsing-remitting MS (RR-MS) and 37 progressive-MS (P-MS) patients. sNfL, plasma total cholesterol (TC), high-density (HDL-C) and low-density (LDL-C) lipoprotein cholesterol, apolipoproteins (Apo), ApoA-I, Apo-II, ApoB, ApoC-II and ApoE were measured at baseline and 5-years. Annual percent changes in whole brain volume (PBVC), gray matter volume (PGMVC) and cortical volume (PCVC) were obtained from MRI at baseline and 5-years. Results sNfL levels at 5-year follow-up were associated with ApoE at follow-up (p = 0.014), age at follow-up, body mass index (p < 0.001) and RR vs. P-MS status at follow-up. APOE4 allele was associated with greater sNfL levels at 5-years (p = 0.022) and pronounced in the P-MS group. PGMVC and PCVC were associated with percent changes in HDL-C (p = 0018 and p < 0.001, respectively) and ApoA-I (p = 0.0073 and p = 0.006). PGMVC and PCVC remained associated with percent change in HDL-C (p = 0.0024 and p < 0.001, respectively) after sNfL was included as a predictor. Conclusions HDL-C percent change is associated with decreased gray matter atrophy after adjusting for baseline sNfL.