Background: Neonatal hypoglycaemia is a common metabolic disorder that may cause brain damage, most visible in the occipital region on MRI. However, it is not known whether neonatal hypoglycaemia is associated with long term changes in brain growth. Therefore, we compared brain volumes and cortical thickness at nine years of age between those who had and had not experienced neonatal hypoglycaemia. Methods: Children born at risk of neonatal hypoglycaemia at ≥ 36 weeks’ gestation who took part in a prospective cohort study underwent brain MRI at nine years of age. Brain morphometric measures were computed using an automated pipeline using FreeSurfer. Results: Children who had (N=75) and had not (N=26) experienced neonatal hypoglycaemia had similar combined parietal and occipital lobes volumes at nine years of age. However, those who had experienced neonatal hypoglycaemia had smaller caudate (-0.05%, 95%CI, -0.07 to -0.02; p=0.001) and thalamus (-0.03%, 95%CI, -0.06 to 0.00; p=0.05) as percentage of total brain volume, and thinner occipital lobe cortex (-0.05mm, 95%CI -0.10 to 0.00, p=0.05) than those who had not. Boys who had experienced neonatal hypoglycaemia had smaller caudate volume, while girls had smaller combined parietal and occipital lobe volumes (p=0.02 for interaction). Conclusion: Neonatal hypoglycaemia is associated with reduced size of specific brain regions in mid-childhood in a sex-specific manner.