Coeliac disease (CD) is an immune-mediated systemic disorder triggered by gluten in genetically predisposed patients. The only available treatment is a strict life long gluten-free diet (GFD), which has been linked to a reduced quality of life (QOL) and causes alterations in the gastrointestinal microbiome. Abnormal compositions of the microbiome are now recognized as factors in the pathogenesis of neuropsychological disorders via gut-brain-axis. The aim of this study was to assess the QOL and the mental performance of children and teenagers with CD and compare it to healthy controls (HC). Children between the ages of 6 and 18 years with CD and age-and-sex-matched healthy controls (HC) filled in a questionnaire to assess QOL and performed the Flanker task, a standardized test to assess cognitive performance. A total of 444 children (210 CD patients and 234 HC) were included in the study. CD patients reported feeling statistically significantly more comfortable at school (p = 0.02) and being less exposed to bullying (p = 0.01); otherwise, no difference in QOL and sleep pattern was found compared to HC. The analysis of Flanker task revealed no difference in accuracy (HC: mean 0.97, CI 0.96-0.97; CD patients: mean 0.96, CI 0.96-0.97; p = 0.79), but there was a difference in reaction time (HC: mean 495.4 ms, CI 476.34-514.46; CD patients: mean 514.03, CI 493.68-534.39; p = 0.19). Children with CD in Switzerland have the same QOL as HC. There was a statistically non-significant difference in reaction time, therefore this study suggests that a GFD is not associated with impaired cognitive function.