Background Reading delays are well documented in children with fragile X syndrome (FXS), but few studies have examined linguistic precursors of reading in this population. This study examined the longitudinal development of phonological awareness and its relationship with basic reading in boys with FXS. Individual differences in genetic, social‐behavioral and environmental factors were also investigated as predictors of phonological awareness. Methods Participants included 54 boys with FXS and 53 typically developing (TD) mental age‐matched peers who completed assessments of phonological awareness, nonverbal intelligence, and reading annually for up to 4 years. FMRP level and autism symptomatology were also measured within the FXS group. Hierarchical linear modeling was used to examine change in phonological awareness over time and its predictors. Linear regression was used to examine phonological awareness as a predictor of word reading. Results Boys with FXS exhibited slower growth than TD peers in phonological awareness only when nonverbal cognitive abilities were not controlled. The rate of change in phonological awareness decreased significantly after age 10 in boys with FXS. Phonological awareness accounted for 18% unique variance in basic reading ability after controlling for nonverbal cognition, with similar relationships across groups. Conclusion Phonological awareness skills in the boys with FXS were commensurate with their nonverbal cognitive abilities, with similar relationships between phonological awareness and reading as observed in the TD mental age‐matched peers. More research is needed to examine potential causal relationships between phonological awareness, other language skills, and reading abilities in individuals with FXS and other neurodevelopmental disorders.