Background: There is scarce and conflicting evidence on medium- to long-term effects of prolonged breastfeeding on child behavior. Method: A population-based birth cohort study started in 2004 in the city of Pelotas, Southern Brazil. Children were followed up at 3, 12, 24, and 48 months and 6 years of age. Breastfeeding duration was determined based on information collected around the time of weaning. Psychiatric disorders were assessed using the Development and Well-Being Assessment (DAWBA). Children who were never breastfed were excluded from the analysis. Crude and adjusted analyses were performed using Poisson regression with robust variance. Results: Data on breastfeeding and mental health at the age of 6 years were available for 3377 children. Prevalence of breastfeeding for 24–35 months and ≥36 months was 16.1% (95% CI: 14.8–17.3) and 8.1% (95% CI: 7.2–9.1), respectively. Prevalence of psychiatric disorders among those who were breastfed for <24 months, 24–35 months and ≥36 months was 12.4% (95% CI: 11.1–13.7), 13.1% (95% CI: 10.4–16.2) and 12.3% (95% CI: 8.7–16.8), respectively. No association was found between breastfeeding for 24 months or more and psychiatric disorders among children aged 6 years both in the crude and adjusted analyses. Conclusions: In this cohort there was no association between breastfeeding for 24 months or more and an increased prevalence of psychiatric disorders at the age of 6 years. Studies analyzing the medium- and long-term effects of prolonged breastfeeding for 2 years or more are scarce and further research is needed regarding this practice.