The World Health Organization (WHO) recommends praziquantel mass drug administration (MDA) to control schistosomiasis in endemic regions. We aimed to quantify recent and lifetime praziquantel coverage, and reasons for non-treatment, at an individual level to guide policy recommendations to help Uganda reach WHO goals. Cross-sectional household surveys (n = 681) encompassing 3208 individuals (adults and children) were conducted in 2017 in Bugoto A and B, Mayuge District, Uganda. Participants were asked if they had received praziquantel during the recent MDA (October 2016) and whether they had ever received praziquantel in their lifetime. A multivariate logistic regression analysis with socio-economic and individual characteristics as covariates was used to determine factors associated with praziquantel uptake. In the MDA eligible population (≥5 years of age), the most recent MDA coverage was 48.8%. Across individuals' lifetimes, 31.8% of eligible and 49.5% of the entire population reported having never taken praziquantel. Factors that improved individuals' odds of taking praziquantel included school enrolment, residence in Bugoto B and increasing years of village-residency. Not being offered (49.2%) and being away during treatment (21.4%) were the most frequent reasons for not taking the 2016 praziquantel MDA. Contrary to expectations, chronically-untreated individuals were rarely systematic non-compliers, but more commonly not offered treatment.