Background Nutrition is a fundamental pillar of human life. Women have an increased risk of undernutrition than men. Undernutrition can result in adverse pregnancy outcomes and intergeneration cycle of undernutrition. The aim of this study is to determine the prevalence of undernutrition and the associated socio-economic determinants among adult women of reproductive age in Uganda.  Methods A population based cross-sectional survey was conducted and 4,640 non-pregnant and non-post-partum women aged 20 to 49 were analyzed. Two stage stratified sampling was used to select study participants and data were collected using validated questionnaires. Multivariable logistic regression was used to model the association between socio-economic determinants and stunting and underweight using weighted data in SPSS version 24.  Results The prevalence of underweight and stunting were 6.9% and 1.3% respectively. Women who belonged to middle (aOR = 2.49, 95% CI 1.25-4.99), poorer (aOR = 3.07, 95%CI 1.57–5.97) and poorest wealth index (aOR = 3.60, 95% CI 1.85–7.00) were more likely to be underweight compared to the richest. Belonging to rural residence (aOR = 0.63, 95%CI 0.41–0.96), Western (aOR = 0.30, 95% CI 0.20–0.44), Eastern (aOR = 0.42, 95% CI 0.28–0.63) and Central regions (aOR = 0.42, 95% CI 0.25–0.72) was associated with less odds of being underweight. Region was the only variable significantly associated with stunting. Wealth index was not significantly associated with stunting.  Conclusion The prevalence of undernutrition in Uganda among women is less compared to most of the neighboring countries. There is need to address the socio-economic determinants including poverty, residence and reducing regional inequalities.