Multiple sclerosis and aquaporin-4 antibody neuromyelitis optica spectrum disorders are distinct autoimmune CNS disorders with overlapping clinical features but differing pathology. Multiple sclerosis is primarily a demyelinating disease with the presence of widespread axonal damage, while neuromyelitis optica spectrum disorders is characterized by astrocyte injury with secondary demyelination. Diagnosis is typically based on lesion characteristics observed on standard MRI imaging and antibody testing but can be challenging in patients with in-between clinical presentations. Non-conventional MRI techniques can provide valuable diagnostic information by measuring disease processes at the microstructural level. We used non-conventional MRI to measure markers of axonal loss in specific white matter tracts in multiple sclerosis and neuromyelitis optica spectrum disorders, depending on their relationship with focal lesions. Patients with relapsing-remitting multiple sclerosis (n = 20), aquaporin-4 antibody-associated neuromyelitis optica spectrum disorders (n = 20) and healthy controls (n = 20) underwent a 3T brain MRI, including T1-, T2- and diffusion-weighted sequences, quantitative susceptibility mapping and phase-sensitive inversion recovery sequence. Tractometry was used to differentiate tract fibres traversing through white matter lesions from those that did not. Neurite density index was assessed using neurite orientation dispersion and density imaging model. Cortical damage was evaluated using T1 relaxation rates. Cortical lesions and paramagnetic rim lesions were identified using phase-sensitive inversion recovery and quantitative susceptibility mapping. In tracts traversing lesions, only one out of 50 tracts showed a decreased neurite density index in multiple sclerosis compared with neuromyelitis optica spectrum disorders. Among 50 tracts not traversing lesions, six showed reduced neurite density in multiple sclerosis (including three in the cerebellum and brainstem) compared to neuromyelitis optica spectrum disorders. In multiple sclerosis, reduced neurite density was found in the majority of fibres traversing (40/50) and not traversing (37/50) white matter lesions when compared to healthy controls. A negative correlation between neurite density in lesion-free fibres and cortical lesions, but not paramagnetic rim lesions, was observed in multiple sclerosis (39/50 tracts). In neuromyelitis optica spectrum disorders compared to healthy controls, decreased neurite density was observed in a subset of fibres traversing white matter lesions, but not in lesion-free fibres. In conclusion, we identified significant differences between multiple sclerosis and neuromyelitis optica spectrum disorders corresponding to their distinct pathologies. Specifically, in multiple sclerosis, neurite density reduction was widespread across fibres, regardless of their relationship to white matter lesions, while in neuromyelitis optica spectrum disorders, this reduction was limited to fibres passing through white matter lesions. Further studies are needed to evaluate the discriminatory potential of neurite density measures in white matter tracts for differentiating multiple sclerosis from neuromyelitis optica spectrum disorders.