Emotional stress is associated with some functional gastrointestinal diseases, but its role in aetiology of functional constipation is unclear. This island-wide, questionnaire-based, cross-sectional survey was conducted to assess the association between constipation and emotional stress, in 10-16-year-olds. Constipation was defined using Rome III criteria. Out of 2699 children included in the analysis, 416 (15.4%) had constipation. Constipation was higher in those exposed to stressful events (odds ratio 2.52, p < 0.0001). Separation from the best friend, failure in an examination, severe illness of a family member, loss of job by a parent, frequent punishment by parents and living in an area affected by separatist war remained independently associated with constipation (p < 0.05). In conclusion, constipation was significantly higher in children exposed to stressful life events. Modulation of gut motility through brain-gut axis probably alters colonic transit and ano-rectal functions, causing constipation.