Background: Household air pollution associated with biomass (wood, dung, charcoal, and crop residue) burning for cooking is estimated to contribute to approximately 4 million deaths each year worldwide, with the greatest burden seen in low and middle-income countries. We investigated the relationship between solid fuel type and respiratory symptoms in Uganda, where 96% of households use biomass as the primary domestic fuel. Materials and Methods: Cross-sectional study of 15,405 pre-school aged children living in charcoal or wood-burning households in Uganda, using data from the 2016 Demographic and Health Survey. Multivariable logistic regression analysis was used to identify the associations between occurrence of a cough, shortness of breath, fever, acute respiratory infection (ARI) and severe ARI with cooking fuel type (wood, charcoal); with additional sub-analyses by contextual status (urban, rural). Results: After adjustment for household and individual level confounding factors, wood fuel use was associated with increased risk of shortness of breath (AOR: 1.33 [1.10–1.60]), fever (AOR: 1.26 [1.08–1.48]), cough (AOR: 1.15 [1.00–1.33]), ARI (AOR: 1.36 [1.11–1.66] and severe ARI (AOR: 1.41 [1.09–1.85]), compared to charcoal fuel. In urban areas, Shortness of breath (AOR: 1.84 [1.20–2.83]), ARI (AOR: 1.77 [1.10–2.79]) and in rural areas ARI (AOR: 1.23 [1.03–1.47]) and risk of fever (AOR: 1.23 [1.03–1.47]) were associated with wood fuel usage. Conclusions: Risk of respiratory symptoms was higher among children living in wood compared to charcoal fuel-burning households, with policy implications for mitigation of associated harmful health impacts.