Importance: Cortical lesions contribute to disability in multiple sclerosis (MS) but their impact on regional neurotransmitter levels remains to be clarified. Objective: To test the hypothesis that cortical lesions in MS alter the regional concentrations of the main excitatory and inhibitory neurotransmitters, glutamate and gamma-aminobutyric acid (GABA), in the affected cortex. Design: Prospective, cross-sectional, observational proton MR-spectroscopy (1H-MRS) and structural MRI study at 7T. Setting: Data were collected at a single center between August 2018 and September 2020. Participants: A volunteer sample of 57 MS patients and 38 healthy participants were screened for participation in the study. 50 MS patients and 28 healthy participants were included. In the final cohort, three patients and five healthy participants were excluded due to drop out (n=6) or insufficient data-quality (n=2). Exposures: Two-voxel 7T 1H-MRS covering the right and left sensorimotor hand areas (SM1-HAND) and high-resolution structural brain 7T MRI. Main outcome: Regional concentrations of glutamate and GABA in SM1-HAND and their relation to cortical lesion volume within the MRS voxel. Results: Data from 34 relapsing remitting (RR) and 13 secondary progressive (SP)MS patients (mean +/- standard deviation, 45.1 +/- 12.5 years, 31 female) along with 23 age- and sex-matched healthy participants (44.4 +/- 13 years, 15 female) entered data-analyses. Patient data were pooled to assess the relationship between cortical lesion volume and neurotransmitter levels. Larger cortical lesion volume within SM1-HAND was associated with higher regional glutamate (0.61 +/- 0.21 log(mm3), P=0.005) and lower regional GABA (-0.71 +/- 0.27 log(mm3), P=0.01) concentration. Between-group comparison showed that glutamate concentration within the SM1-voxel was reduced in SPMS patients compared to healthy participants (-0.75 +/- 0.24 mM, P=0.004) and RRMS patients (-0.55 +/- 0.22 mM, P=0.04), while regional GABA levels did not differ among groups. Conclusion: Our results link cortical lesion load in SM1-HAND with regional glutamate and GABA levels in patients with RRMS and SPMS, showing a shift in balance between regional excitatory and inhibitory neurotransmitters towards increased excitation with increasing cortical lesion volume. Between-group comparisons provide preliminary evidence that a progressive disease course may be associated with a decrease in cortical glutamate levels.