A large body of literature demonstrates that different cognitive components related to executive function (EF), such as short-term memory, working memory, and response inhibition, are linked to early academic skills in preschool children. Nevertheless, few studies have focused on the unique contributions of these components to distinctive early numeracy and literacy skills in preschool children. Moreover, most studies have not considered the covariance between these early academic skills in preschool-aged children. The present study examined whether there are differential contributions of visual-spatial and verbal short-term memory, working memory, and response inhibition to specific early numeracy and literacy skills in preschool-aged children, taking into account the covariance among these outcomes. Several seemingly unrelated regression (SUR) analyses were conducted with 419 Chilean preschool-aged children (M = 53.9 months; SD = 4.22). The results show that both response inhibition and verbal short-term memory uniquely predicted all academic outcomes; working memory predicted all early academic skills (with the exception of verbal counting); and visual-spatial short-term memory predicted all numeracy skills and receptive vocabulary. When comparing the marginal effects of the EFs on the outcomes, response inhibition more strongly predicted applied problems than did working memory. Both visual-spatial short-term memory and response inhibition had a greater effect on explaining applied problems, compared to early decoding skills. Implications for teachers and interventions are discussed.