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Recent studies have focused on persistent reading difficulties, but few have investigated students with late-emerging reading difficulties or LRD (i.e., those did not show reading difficulties until later grades). Utilizing a large-scale dataset, we investigated the prevalence of LRD in primary grades and if early executive function (EF) deficits were risk factors of typically developing Kindergarteners and Grade 1 students to have reading difficulties at Grade 2. We found that around 9% students had LRD profiles and the three early EF skills (working memory, shifting, and inhibition) had significant associations with the emergence of LRD. We suggested that future researchers should monitor early EF skills among young readers, and embed EF training into reading instruction to prevent future reading difficulties.