There is dual endemicity of malaria and helminthic infections in low- and middle-income countries. Coinfection with both infectious diseases may have compounding negative effects on the health of school-aged children (SAC) in endemic areas. The prevalence of coinfection with malaria and intestinal helminths, including soil-transmitted helminths, Schistosoma mansoni, and Hymenolepis nana, was assessed among SAC in rural northern Uganda. A school-based cross-sectional study was conducted at four randomly selected schools from June 2 to June 10, 2025 in Nwoya District, Uganda. Children aged 5-18 years provided stool and blood samples, and were surveyed to assess demographic, environmental, and health-related factors. Intestinal helminth diagnosis was performed using a modified Kato-Katz method (Odongo-Aginya stain); malaria was detected using Plasmodium falciparum (P. falciparum) histidine-rich protein 2 rapid diagnostic tests (RDTs) and blood smears. Overall, 190 SAC with a median age of 13 years were enrolled. Although 75.3% (n = 143) of SAC tested positive for P. falciparum on an RDT, only 13.2% (n = 25) had microscopically detected parasitemia. Intestinal helminth infections were uncommon and involved Ascaris lumbricoides (0.5%; n = 1), Hymenolepis nana (1.6%; n = 3), and Schistosoma mansoni (1.1%; n = 2). All SAC with intestinal helminth infections (3.2%; n = 6) had positive malaria RDT results. The high rate of malaria RDT positivity with negative blood smears may be due to persistent antigenemia post-treatment or false negative blood smear results due to chronic low-grade parasitemia. The low rate of malaria-helminth coinfection among SAC observed in the present study is supported by other recent studies in Uganda and suggests a high efficacy of national mass drug administration programming for the control of intestinal helminths.