Long‐chain polyunsaturated fatty acids (LCPUFA) have been shown to be necessary for early retinal and brain development, but long‐term cognitive benefits of LCPUFA in infancy have not been definitively established. The present study sought to determine whether LCPUFA supplementation during the first year of life would result in group differences in behavior and event‐related potentials (ERPs) while performing a task requiring response inhibition (Go/No‐Go) at 5.5 years of age. As newborns, 69 children were randomly assigned to infant formulas containing either no LCPUFA (control) or formula with 0.64% of total fatty acids as arachidonic acid (ARA; 20:4n6) and various concentrations of docosahexaenoic acid (DHA; 22:6n3) (0.32%, 0.64% or 0.96%) for the first 12 months of life. At 5.5 years of age, a task designed to test the ability to inhibit a prepotent response (Go/No‐Go) was administered, yielding both event‐related potentials (ERPs) and behavioral data. Behavioral measures did not differ between groups, although reaction times of supplemented children were marginally faster. Unsupplemented children had lower P2 amplitude than supplemented children to both Go and No‐Go conditions. N2 amplitude was significantly higher on No‐Go trials than Go trials, but only for supplemented children, resulting in a significant Group × Condition interaction. Topographical analysis of the ERPs revealed that the LCPUFA‐supplemented group developed a novel period of synchronous activation (microstate) involving wider anterior brain activation around 200 ms; this microstate was not present in controls. These findings suggest that LCPUFA supplementation during the first 12 months of life exerts a developmental programming effect that is manifest in brain electrophysiology. A video abstract of this article can be viewed at: https://www.youtube.com/watch?v=oM2leg4sevs. This research is part of a longitudinal study in which infants were randomized to formula with or without long‐chain polyunsaturated fatty acid (LCPUFA) supplementation during the first year of life and followed to age 9 years. The results reported here show differences in brain electrophysiology to a Go/No‐Go task when the children were between 5 and 6 years of age. Children who were supplemented in early life show significant event‐related potential (ERP) amplitude differences between the Go and No‐Go conditions that were not evident in the control group. Further, microstate analysis confirmed the significant condition difference, only in the LCPUFA‐supplemented group and the between group difference for the No‐Go condition, showing greater anterior activation for this microstate. These results, combined with previously reported measures of cognitive development in early childhood, suggest that LCPUFA supplementation in early life has a long‐term programming effect.