Background: Cortical lesion subtypes’ occurrence and distribution across networks may shed light on cognitive impairment (CI) in multiple sclerosis (MS). Methods: In 332 people with MS, lesions were classified as intracortical, leukocortical or juxtacortical based on artificially generated double inversion-recovery images. Results: CI-related leukocortical lesion count increases were greatest within sensorimotor and cognitive networks ( p < 0.001). Only intracortical lesion count could distinguish between cognitive groups ( p = 0.024). Effect sizes were two- to four-fold larger than differences between MS phenotypes. Conclusion: In CI-MS, leukocortical lesions predominate, whereas intracortical lesions distinguish cognitive groups. Lesions’ grey matter (GM) involvement might be decisive for cognition in MS, surpassing overall disease burden.