Well-built housing limits mosquito entry and can reduce malaria transmission. The association between community-level housing and malaria burden in Uganda was assessed using data from randomly selected households near 64 health facilities in 32 districts. Houses were classified as ‘improved’ (synthetic walls and roofs, eaves closed or absent) or ‘less-improved’ (all other construction). Associations between housing and parasitaemia were made using mixed effects logistic regression (individual-level) and multivariable fractional response logistic regression (community-level), and between housing and malaria incidence using multivariable Poisson regression. Between November 2021 and March 2022, 4,893 children aged 2–10 years were enrolled from 3,518 houses; of these, 1,389 (39.5%) were classified as improved. Children living in improved houses had 58% lower odds (adjusted odds ratio = 0.42, 95% CI 0.33–0.53, p < 0.0001) of parasitaemia than children living in less-improved houses. Communities with > 67% of houses improved had a 63% lower parasite prevalence (adjusted prevalence ratio 0.37, 95% CI 0.19–0.70, p < 0.0021) and 60% lower malaria incidence (adjusted incidence rate ratio 0.40, 95% CI 0.36–0.44, p < 0.0001) compared to communities with < 39% of houses improved. Improved housing was strongly associated with lower malaria burden across a range of settings in Uganda and should be utilised for malaria control.