We describe the prevalence and risk factors for protracted bacterial bronchitis (PBB) following healthcare presentation for an acute cough illness in children. Data from three studies of the development of chronic cough (CC) in children were combined. PBB was defined as a wet cough of at least 4-weeks duration with no identified specific cause of cough that resolved following 2–4 weeks of appropriate antibiotics. Anterior nasal swabs were tested for 17 viruses and bacteria by polymerase chain reaction. The study included 903 children. Childcare attendance (adjusted relative risk (aRR) = 2.32, 95% CI 1.48–3.63), prior history of chronic cough (aRR = 2.63, 95% CI 1.72–4.01) and age <2-years (<12-months: aRR = 4.31, 95% CI 1.42–13.10; 12-<24 months: aRR = 2.00, 95% CI 1.35–2.96) increased risk of PBB. Baseline diagnoses of asthma/reactive airways disease (aRR = 0.30, 95% CI 0.26–0.35) or bronchiolitis (aRR = 0.15, 95% CI 0.06–0.38) decreased risk. M. catarrhalis was the most common organism (52.4%) identified in all children (PBB = 72.1%; no PBB = 50.2%, p < 0.001). We provide the first data on risks for PBB in children following acute illness and a hypothesis for studies to further investigate the relationship with wheeze-related illnesses. Clinicians and parents/guardians should be aware of these risks and seek early review if a wet cough lasting more than 4-weeks develops the post-acute illness.