Human milk oligosaccharides (HMOs), whose compositions vary between secretor and non-secretor mothers, protect breastfeeding children against various diseases. We investigated the relationship between HMOs in Ugandan secretor mothers and malaria outcomes in their children. Malaria outcomes in breastfeeding children followed up over seven months were classified as malaria-free and asymptomatic, mild, or severe malaria. A single human milk sample collected from each mother was analyzed for HMOs. Significantly higher 2’fucosyllactose (2’FL) and lacto-N-fucopentaose I (LNFP I) concentrations were observed in mothers of malaria-free children, and significantly higher lacto-N-tetraose (LNT) concentrations were observed in mothers of children with asymptomatic malaria. Concentrations of five HMOs, 3-fucosyllactose (3 FL), 3’sialyllactose (3’SL), difucosyllactose (DFLac), lacto-N-fucopentaose II (LNFP II), and sialyllacto-N-tetraose b (LSTb); and two HMOs, difucosyllacto-N-tetrose (DFLNT) and fucosyllacto-N-hexaose (FLNH) were significantly higher in mothers of malaria-infected children and children with severe malaria, respectively. Sex-dependent associations were observed for some HMOs.