Objective: To estimate the prevalence of exclusive breastfeeding during maternity hospital stay (outcome) and to analyze the association between delivery in a Baby-Friendly Hospital (BFH) and the outcome. The hypothesis is that accreditation to this program improves exclusive breastfeeding during maternity hospital stay. Exclusive breastfeeding is essential in reducing neonatal morbidity and mortality. Methods: This study is based on secondary data collected by the “Birth in Brazil: National Survey into Labour and Birth”, a population-based study, conducted with 21,086 postpartum women, from February 1, 2011, to October 31, 2012, in 266 hospitals from all five Brazilian regions. Face-to-face interviews were conducted mostly within the first 24 hours after birth, regarding individual and gestational characteristics, prenatal care, delivery, newborn’s characteristics, and breastfeeding at birth. A theoretical model was created, allocating the exposure variables in three levels based on their proximity to the outcome. This hierarchical conceptual model was applied to perform a multiple logistic regression (with 95%CI and p < 0.05). Results: In this study, 76.0% of the babies were exclusively breastfed from birth until the interview. Babies born in public (AOR = 1.73; 95%CI: 1.10–2.87), mixed (AOR = 2.48; 95%CI: 1.35–4.53) and private (AOR = 5.54; 95%CI: 2.38–12.45) BFHs were more likely to be exclusively breastfed during maternity hospital stay than those born in non–BFHs, as well as those born by vaginal birth (AOR = 2.16; 95%CI: 1.79–2.61), with adolescent mothers (AOR = 1.83; 95%CI: 1.47–2.26) or adults up to 34 years old (AOR =1 .31; 95%CI: 1.13–1.52), primiparous women (AOR = 1.51; 95%CI: 1.34–1.70), and mothers living in the Northern region of Brazil (AOR = 1.99; 95%CI: 1.14–3.49). Conclusions: The Baby-Friendly Hospital Initiative promotes exclusive breastfeeding during hospital stay regarding individual and hospital differences.