This study aimed to establish quantitative muscle MRI as an endpoint for monitoring disease progression in GNE myopathy clinical trials. MRI of the thighs was performed on 14 patients with GNE myopathy at baseline and 6 months. The cross-sectional area of predefined muscle compartments was measured and muscle/fat composition was differentiated using thresholding. A statistically significant decrease in muscle area was found only in the left posterior and medial thigh compartments within 6 months, consistent with expected slow disease progression. Further follow-up is needed in this ongoing study to better detect changes in this rare, slowly progressive disorder. Quantitative muscle MRI may be a useful outcome measure for GNE myopathy clinical trials.