In this study, we reported two major findings regarding the roles of CPEB1 under physiological conditions and in the FXS cell model: (i) CPEB1 controlled Fmr1 mRNA intracellular localization and post-transcriptionally regulated Fmr1 expression, and (ii) CPEB1 was involved in mitochondrial functions through modulation of the mRNA expression levels of mitochondria-related genes and HSPA9 localization in FMR1 knockdown Neuro2a cells. The gene discussed is HSPA9; the disease is fragile X syndrome.