A cross-sectional study to assess the prevalence of intestinal helminth infections and nutritional status of primary school children was conducted in the Wakiso district in Central Uganda. A total of 432 primary school children aged 6–14 years were randomly selected from 23 schools. Anthropometric measurements of weight, height, MUAC were undertaken and analyzed using AnthroPlus software. Stool samples were examined using a Kato-Katz method. The prevalence of stunting, underweight and moderate acute malnutrition (MAM) was 22.5%, 5.3% and 18.5% respectively. Males had a threefold risk of being underweight (OR 3.2, 95% CI 1.17–9.4, p = 0.011) and 2 fold risk of suffering from MAM (OR 2.1, 95% CI 1.21–3.48, p = 0.004). Children aged 10–14 years had a 2.9 fold risk of stunting (OR 2.9, 95% CI 1.37–6.16, p = 0.002) and 1.9 risk of MAM (OR 1.9, 95% CI 1.07–3.44, p = 0.019). Attending urban slum schools had 1.7 fold risk of stunting (OR 1.7, 95% CI 1.03–2.75, p = 0.027). Rural schools presented a twofold risk of helminth infection (OR 1.95, 95% CI 1.12–3.32, p = 0.012). The prevalence of helminth infections was (10.9%), (3.1%), (1.9%), (0.2%) for hookworm, Trichuria trichiura, Schistosoma mansoni and Ascaris lumbricoides, respectively. The study revealed that 26.6%, 46% and 10.3% of incidences of stunting, underweight and MAM respectively were attributable to helminth infections.