Human milk oligosaccharides (HMOs) are one of the most abundant solid components in a mother’s milk. Animal studies have confirmed a link between early life exposure to HMOs and better cognitive outcomes in the offspring. Human studies on HMOs and associations with later child cognition are scarce. In this preregistered longitudinal study, we investigated whether human milk 2′-fucosyllactose, 3′-sialyllactose, 6′-sialyllactose, grouped fucosylated HMOs, and grouped sialylated HMOs, assessed during the first twelve postnatal weeks, are associated with better child executive functions at age three years. At infant age two, six, and twelve weeks, a sample of human milk was collected by mothers who were exclusively (n = 45) or partially breastfeeding (n = 18). HMO composition was analysed by use of porous graphitized carbon-ultra high-performance liquid chromatography–mass spectrometry. Executive functions were assessed at age three years with two executive function questionnaires independently filled in by mothers and their partners, and four behavioural tasks. Multiple regression analyses were performed in R. Results indicated that concentrations of 2′-fucosyllactose and grouped fucosylated HMOs were associated with better executive functions, while concentrations of grouped sialylated HMOs were associated with worse executive functions at age three years. Future studies on HMOs that sample frequently during the first months of life and experimental HMO administration studies in exclusively formula-fed infants can further reveal associations with child cognitive development and uncover potential causality and sensitive periods.