In utero exposure to household air pollution (HAP) from polluting cooking fuels has been linked to adverse pregnancy outcomes including low birthweight (LBW). No previous study in Uganda has attempted to investigate the association between the different types of biomass cooking fuels and LBW. This study was conducted to investigate the association between wood and other biomass cooking fuel use with increased risk of LBW, using the 2016 Uganda Demographic and Health Survey for 15,270 live births within five years prior to interview. LBW, defined as birthweight of <2500 g, was estimated from maternal recall and health cards. Association between household exposure to the different solid biomass cooking fuels and LBW was determined using multivariable logistic regression. Biomass cooking fuels were used in 99.6% of the households, with few (0.3%) using cleaner fuels and 0.1% with no cooking, while the prevalence of LBW was 9.6% of all live-births. Although the crude analysis suggested an association between wood fuel use and LBW compared to other biomass and kerosene fuel use (AOR: 0.82; 95% CI: 0.67–1.00), after adjusting for socio-demographic and obstetric factors, no association was observed (AOR: 0.94; 95% CI: 0.72–1.22). LBW was significantly more likely among female neonates (AOR: 1.32 (95% CI: 1.13–1.55) and neonates born to mothers living in larger households (AOR: 1.03; 95% CI: 1.00–1.07). LBW was significantly less likely among neonates delivered at term (AOR: 0.39; 95% CI: 0.31–0.49), born to women with secondary or tertiary level of education (AOR: 0.80; 95% CI: 0.64–1.00), living in households with a higher wealth index (AOR: 0.69; 95% CI: 0.50–0.96), Eastern (AOR: 0.76; 95% CI:0.59–0.98) and Northern (AOR: 0.75; 95% CI: 0.57–0.99) regions. The study findings suggest inconclusive evidence regarding the association between the use of wood compared to other biomass and kerosene cooking fuels and risk of LBW. Given the close observed association between socioeconomic status and LBW, the Ugandan government should prioritize public health actions which support female education and broader sustainable development to improve household living standards in this setting.