Objective To examine bi-directional associations between a child’s fussy eating behavior and functional constipation. Study design Participants are 4823 children enrolled in a prospective cohort study from pregnancy onwards. We assessed fussy eating at 4 years of age with The Child Eating Behavior Questionnaire. Functional constipation was assessed using ROME II and III criteria with parental questionnaires at 2, 3, 4, and 6 years of age. Results Higher food fussiness at 4 years of age was associated with a higher risk of functional constipation at both ages 4 years (OR 1.30, 95% CI 1.20; 1.42, p < .001 per SD increase) and 6 years (OR 1.12, 95% CI 1.03; 1.23, p < .05 per SD increase). The converse was also observed: previous constipation predicted a higher risk of being a fussy eater at 4 years of age (constipation at 2-years: OR 2.05, 95% CI 1.43; 2.94, p < .001; constipation at 3 years: OR 1.72, 95% CI 1.26; 2.35, p < .001). Path analyses confirmed that the association between fussy eating and functional constipation was indeed bi-directional, showing that functional constipation at 3 years of age predicted fussy eater classification at 4 years of age (β = 0.06, p < .001), which in turn predicted functional constipation at 6 years of age (β = 0.08, p < .001) independently of each other. Conclusion A vicious cycle might develop in which children with functional constipation develop unhealthy eating behavior, that in turn increases the risk of functional gastrointestinal disease.