Auditory processing of temporal information in speech is sustained by synchronized firing of neurons along the entire auditory pathway. In school-aged children and adults with dyslexia, neural synchronization deficits have been found at cortical levels of the auditory system, however, these deficits do not appear to be present in pre-reading children. An alternative role for subcortical synchronization in reading development and dyslexia has been suggested, but remains debated. By means of a longitudinal study, we assessed cognitive reading-related skills and subcortical auditory steady-state responses (80 Hz ASSRs) in a group of children before formal reading instruction (pre-reading), after 1 year of formal reading instruction (beginning reading), and after 3 years of formal reading instruction (more advanced reading). Children were retrospectively classified into three groups based on family risk and literacy achievement: typically developing children without a family risk for dyslexia, typically developing children with a family risk for dyslexia, and children who developed dyslexia. Our results reveal that children who developed dyslexia demonstrate decreased 80 Hz ASSRs at the pre-reading stage. This effect is no longer present after the onset of reading instruction, due to an atypical developmental increase in 80 Hz ASSRs between the pre-reading and the beginning reading stage. A forward stepwise logistic regression analysis showed that literacy achievement was predictable with an accuracy of 90.4% based on a model including three significant predictors, that is, family risk for dyslexia (R = 0.31), phonological awareness (R = 0.23), and 80 Hz ASSRs (R = 0.26). Given that: (1) abnormalities in subcortical ASSRs preceded reading acquisition in children who developed dyslexia; and (2) subcortical ASSRs contributed to the prediction of literacy achievement, subcortical auditory synchronization deficits may constitute a pre-reading risk factor in the emergence of dyslexia.